Document:

<PAGE>

                                                                   EXHIBIT 10.15

                              SETTLEMENT AGREEMENT

     This is a Settlement Agreement entered into March 7, 2000 (the "Effective
Date") by and between:

     Scriptgen Pharmaceuticals, Inc., a Delaware corporation having a principal
place of business at 610 Lincoln Street, Waltham, MA 02451 ("Scriptgen"); and

     3-Dimensional Pharmaceuticals, Inc., a Delaware corporation having a
principal place of business at 665 Stockton Drive, Exton, PA 19341 ("3DP").

     WHEREAS, Scriptgen is the owner of U.S. Patent 5,585,277 ("the `277
patent'"), and U.S. Patent No. 5,679,582 ("the `582 patent'");

     WHEREAS on October 13, 1998, Scriptgen filed an action in the United States
District Court for the District of Delaware, captioned Scriptgen
Pharmaceuticals, Inc. v. 3-Dimensional Pharmaceuticals, Inc., Civil Action No.
98-583-GMS, in which Scriptgen has asserted claims against 3DP for infringement
of the `277 patent and the `582 patent and 3DP has asserted defenses and
counterclaims against Scriptgen including the non-infringement, invalidity, and
unenforceability of the `277 patent and the `582 patent ("the Action"); and

     WHEREAS Scriptgen and 3DP desire to settle all claims that have been raised
in the Action and wish to avoid any further controversy between them as set
forth herein.

     NOW THEREFORE, in consideration of the mutual covenants and undertakings of
the parties, Scriptgen and 3DP agree as follows:

1.   DEFINITIONS

1.1  "Affiliate" shall mean an entity that directly, or indirectly through one
     or more intermediaries, controls, or is controlled by, or is under common
     control with, 3DP or Scriptgen, as applicable; provided further that
     "control(s)(led)" as used in this Section shall mean ownership by a third
     party, not including a venture capital fund or group of venture capital
     funds, of at least fifty percent (50%) of the equity capital of such
     entity.

1.2  "Atlas Technology" shall mean the methods and processes generally disclosed
     in the specifications and claims of the `277 patent, the `582 patent and/or
     Scriptgen International Application No. PCT/US96/19698.

1.3  "Calendar Quarter" shall mean each three month period, or any portion
     thereof, ending on March 31, June 30, September 30 and December 31.

1.4  "Development Compound" shall mean a compound that has entered pre-clinical
     regulatory drug safety studies conducted under good laboratory practice
     (GLP) guidelines.
<PAGE>

1.5  "Hepatitis C Virus Field" shall mean any program(s) whose intent is to
     discover or develope a drug that exerts a therapeutic effect in Hepatitis C
     Virus Infection.

1.6  "Infection" shall mean the field of treatment with, research on, and/or
     development of drugs whose principal aim is to treat or cure infectious
     disease in humans.
1.7  "Method Claims" shall mean any claim in a patent or application to a
     process or method and shall not include any claim to a product or
     apparatus.

1.8  "Net Revenues" shall mean the revenues actually received by a party from
     the offering or provision of drug screening services or from the sale of
     drug compounds, after allowing deductions for sales, use and other similar
     taxes (excluding taxes based on such party's income or revenues), the legal
     incidence of which is on such party, returns and other credits.

1.9  "Restriction Period" shall mean the period of time beginning from the
     Effective Date and ending on the third (3rd) anniversary of the Effective
     Date.

1.10 "Scriptgen" shall mean Scriptgen Pharmaceuticals, Inc., its present and
     future Affiliates, and any entity in which Scriptgen Pharmaceuticals, Inc.
     owns or controls a majority interest.

1.11 "ThermoFluor Deal" shall mean a business arrangement between 3DP and a
     third party collaborator, for any duration of time, involving the use of
     3DP's ThermoFluor(R) Screening Technology at one or more research sites
     anywhere in the world and operated by 3DP and/or such third party
     collaborating with 3DP.

1.12 "ThermoFluor Screening Technology" shall mean the methods, processes and
     apparatus generally disclosed in the specifications and claims of U.S.
     Patent No. 6,020,141 and/or allowed U.S. Patent Application Serial no.
     08/853,459.

1.13 "3DP" shall mean 3-Dimensional Pharmaceuticals, Inc., its present and
     future Affiliates, and any entity in which 3-Dimensional Pharmaceuticals,
     Inc. owns or controls a majority interest.

1.14 "3DP Internal Program(s)" shall mean drug discovery and/or development
     program(s) in any therapeutic field conducted for and by 3DP on-site at a
     3DP facility.

2.   FINANCIAL PAYMENT AND RELEASE

2.1  In order to reimburse Scriptgen for legal fees and expenses incurred by
     Scriptgen in the Action, 3DP agrees to make a non-refundable payment to
     Scriptgen of five hundred thousand United States dollars ($500,000) on
     each of the following dates: (a) the Effective Date; (b) six (6) months
     after the Effective Date; and (3) the first (1st) anniversary of the
     Effective Date.

2.2  Each payment shall be by wire transfer to [**]. A letter confirming the
     transfer shall be delivered to Scriptgen's counsel, DARBY & DARBY, PC, 805
     Third Avenue, New York, NY 10022, by overnight courier.

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission.  The omitted
portions have been filed separately with the Commission.

                                      -2-
<PAGE>

2.3  Upon full execution of this Agreement by the parties and receipt by
     Scriptgen of the initial non-refundable payment specified in Section 2.1(a)
     above, Scriptgen for itself and for its shareholders, officers, directors,
     agents, representatives and all persons and entities claiming under or
     through it, releases 3DP, and its shareholders, employees, agents,
     officers, directors, representatives, customers, suppliers, manufacturers,
     partners and distributors, from any and all claims of infringement of the
     `277 patent and the `582 patent, and from all injuries and damages which
     may have resulted therefrom, whether now known, unforeseen, unanticipated
     or latent which Scriptgen ever had, now has, or hereafter can, shall or may
     have, by reason of any act, omission or occurrence prior to the Effective
     Date.

2.4  3DP, for itself and for its shareholders, officers, directors, agents,
     representatives and all persons and entities claiming under or through it,
     releases Scriptgen and its shareholders, employees, agents, officers,
     directors, representatives, customers, suppliers, manufacturers, partners
     and distributors, from any and all claims of any kind and from all injuries
     and damages which may have resulted therefrom, whether now known,
     unforeseen, unanticipated or latent which 3DP ever had, now has, or
     hereafter can, shall or may have, by reason of any act, omission or
     occurrence prior to the Effective Date with respect to the subject matter
     of the Action.

2.5  The parties will direct their attorneys to sign the Stipulated Order of
     Dismissal attached hereto as Exhibit A simultaneously with signing this
     Agreement and to cause their respective attorneys to file the signed
     Stipulated Order of Dismissal with the Court in the Action within five (5)
     days after the full execution of this Agreement and the receipt by
     Scriptgen of the initial non-refundable payment specified in Section 2.1(a)
     above.

2.6  The parties each agree that within sixty (60) days after entry of the
     Stipulated Order of Dismissal, they will each return to the other party, in
     accordance with paragraph sixteen (16) of the Stipulation and Order
     Governing the Protection and Exchange of Confidential Material in the
     Action, dated March 23, 1999, or certify the destruction of, all
     confidential documents that were produced by the other party during the
     course of the Action.

3.   LICENSE GRANT BY SCRIPTGEN TO 3DP

3.1  In settlement of the Action, Scriptgen hereby grants to 3DP beginning on
     the Effective Date, and subject to Sections 3.2 through 3.11, a perpetual,
     non-exclusive, worldwide, fully-paid license, with the right to sub-
     license, under the `277 patent, the `582 patent, and any patents issuing
     from Scriptgen International Application No. PCT/US96/19698, any and all
     continuing applications, divisional applications, continuation-in-part
     applications, reissues, extensions, renewals and reexaminations thereof,
     and any U.S. and foreign counterparts thereof. In addition, Scriptgen
     agrees not to file any future patent infringement actions against 3DP for
     3DP's use of ThermoFluor Screening Technology that is consistent with the
     terms of this Agreement.

                                      -3-
<PAGE>

3.2  3DP shall not have the right to assign the license granted herein
     except as part of the sale of its ThermoFluor Screening Technology or
     business, the sale of substantially all the capital stock or assets of the
     corporation, or the merger or consolidation of the corporation.

3.3  During the Restriction Period, 3DP shall be permitted to enter into only
     one (1) ThermoFluor Deal, including the right to sub-license, and including
     unrestricted sales of ThermoFluor Screening Technology instruments, where
     the principal focus of such business arrangement is Infection, provided
     however that such ThermoFluor Deal may not involve the Hepatitis C Virus
     Field, nor involve more than three (3) other anti-viral targets.

3.4  3DP shall be able to freely secure any partnerships or other business
     arrangements involving ThermoFluor Screening Technology, except that during
     the Restriction Period the principal focus may not be Infection and 3DP
     shall not grant any sublicenses for Infection during the Restriction
     Period, except as permitted under Sections 3.3 and 3.10 of this Agreement.
     In the event that a partner or other third party requests that 3DP screen,
     during the Restriction Period, multiple targets which include Intended
     Infection targets, 3DP shall inform such party that it cannot screen such
     Infection targets, but shall disclose that such screening can be conducted
     by Scriptgen. Scriptgen shall pay to 3DP [**] of all Net Revenues received
     during the first year of an agreement which demonstrably resulted from such
     an introduction by 3DP.

3.5  During the Restriction Period, Scriptgen may refer to 3DP any third parties
     that have requested that Scriptgen screen multiple targets to identify
     leads or drugs that are effective in any field other than Infection. In
     such event, 3DP shall pay to Scriptgen [**] of all Net Revenues received
     during the first year of an agreement which demonstrably resulted from such
     an introduction by Scriptgen, if such third party or its Affiliates were
     not previously contacted by 3DP.

3.6  3DP shall be free to use ThermoFluor Screening Technology without
     restriction in any 3DP Internal Program, except in the Hepatitis C Virus
     Field during the Restriction Period, and to license or transfer, in any
     manner, any compounds discovered or optimized through such use of
     ThermoFluor Screening Technology. 3DP shall not use ThermoFluor Screening
     Technology in the Hepatitis C Virus Field during the Restriction Period.

3.7  In the event that 3DP uses ThermoFluor Screening Technology in a 3DP
     Internal Program that leads to the designation, during the Restriction
     Period, of a Development Compound that leads to a drug in Infection, 3DP
     shall pay to Scriptgen a sliding-scale royalty based on 3DP's Net Revenues
     from the sale of such drug by 3DP, as follows:

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission.  The omitted
portions have been filed separately with the Commission.

                                      -4-
<PAGE>

                            Category                                Royalty
                            --------                                -------

All anti-infectives, except anti-virals:

[**]                                                                  [**]

[**]                                                                  [**]

All anti-virals                                                       [**]

Nothing in this Section 3.7 shall be construed as giving 3DP the right to use
ThermoFluor Screening Technology in the Hepatitis C Virus field during the
Restriction Period.

3.8  The maximum aggregate amount of all royalty payments made under Section
     3.7, on a cumulative basis including all such 3DP Internal Programs, shall
     not exceed five million United States dollars ($5,000,000).

3.9  In the event that 3DP uses ThermoFluor Screening Technology, in a 3DP
     Internal Program that leads to the designation, during the Restriction
     Period, of a Development Compound that leads to a drug in Infection, and
     3DP subsequently licenses or sells the rights to such drug to a third
     party, 3DP shall pay to Scriptgen [**] in the case of anti-infectives
     (excluding anti-virals), or [**] in the case of anti-virals, of the up-
     front cash payments or sales price received by 3DP from such transaction.
     The maximum amount of all such payments in aggregate shall not exceed two
     million United States dollars ($2,000,000). Notwithstanding the foregoing,
     if any such up-front payments are in the form of an investment in equity
     securities of 3DP, the amount of such investment, calculated on a per share
     basis, that is in excess of [**] of the amount per share paid in the last
     3DP equity financing (or, if 3DP is public, [**] of the closing price
     immediately prior to the transaction) shall be deemed to be an "up-front
     payment" for purposes of this calculation.

3.10 There shall be no limitations on sales, licenses (including the right to
     grant sublicenses limited to use of the ThermoFluor Screening Technology
     instruments), or leases of ThermoFluor Screening Technology instruments,
     except that during the Restriction Period, in the therapeutic field of
     Infection, 3DP may only sell, license (including the right to grant
     sublicenses limited to use of ThermoFluor Screening Technology
     instruments), or lease ThermoFluor Screening Technology instruments as part
     of the permitted ThermoFluor Deal in Infection specified in Section 3.3
     above.

3.11 The license of Section 3.1 shall not be deemed to grant a license,
     directly, or by implication or otherwise, under any know-how, copyright,
     trademark, or other intellectual property right.

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission.  The omitted
portions have been filed separately with the Commission.

                                      -5-
<PAGE>

4.   THE RESTRICTION PERIOD

4.1  The restrictions of Sections 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9 and 3.10 on
     the perpetual, nonexclusive, worldwide, fully-paid license granted by
     Scriptgen in Section 3.1 above, shall terminate on the earlier of:

     (a)  The end of the Restriction Period; or

     (b)  Any finding of invalidity or unenforceability of claims 1 and 17 of
          the 277 patent and claims 1, 3, 5, 20, 23 and 26 of the 582 patent by
          the USPTO or by a court of competent jurisdiction from either of which
          an appeal can no longer be taken.

5.  LICENSE GRANT BY 3DP TO SCRIPTGEN

5.1  (a)  In settlement of the Action, 3DP hereby grants to Scriptgen beginning
          on the Effective Date a perpetual, non-exclusive, worldwide, fully
          paid license, under any Method Claims found in: (a) U.S. Patent No.
          6,020,141; (b) any U.S. patents issuing from allowed U.S. Patent
          Application Serial No. 08/853,459; (c) any patents issuing from any
          and all continuing applications, divisional applications,
          continuation-in-part applications of said `141 patent, said `459
          application and/or the application on which said `141 patent was
          granted, and any reissues, extensions, renewals and reexaminations of
          such patents or patent applications; and/or (d) any foreign
          counterparts of the patents in (a), (b) and (c). The license granted
          to Scriptgen herein shall include the right to sublicense solely in
                                                                    ------
          the field of Infection. In addition, 3DP agrees not to file any future
          patent infringement actions against Scriptgen for Scriptgen's use of
          Atlas Technology that is consistent with the terms of this Agreement.

     (b)  During the first three years after the Effective Date, screening
          collaborations conducted by Scriptgen on behalf of third parties
          outside the field of Infection shall be conducted on-site at a
          Scriptgen facility only and shall not exceed ten (10) such screening
          collaborations; provided however that this limitation shall expire at
          the end of the three-year period.

5.2  The license of Section 5.1 shall not be deemed to grant a license, directly
     or by implication or otherwise, under any know-how, copyright, trademark,
     or any other intellectual property right.

5.3  Scriptgen shall not have the right to assign the license granted herein
     except as part of the sale of its Atlas Technology or business, the sale of
     substantially all the capital stock or assets of the corporation, or the
     merger or consolidation of the corporation.

6.  ROYALTY PAYMENTS, RECORDS AND INSPECTION

6.1  All payments based upon Net Revenues payable hereunder ("Royalty" or
     "Royalties") which have accrued in any Calendar Quarter shall be made
     within forty-five (45) days after the end of such Calendar Quarter.

                                       6
<PAGE>

6.2  Each party shall keep accurate records and books of account in sufficient
     detail to enable all Royalty payments to be determined. A written report
     shall accompany each Royalty payment setting forth in reasonable detail,
     for the applicable Calendar Quarter, the total Royalties that are to be
     paid to a party hereunder and the other party's calculation thereof.

6.3  Upon ten (10) days' prior written notice to a party and during normal
     business hours, but not more frequently than annually, an independent
     auditor of nationally recognized standing agreed to by both parties and
     paid for by the other party may inspect such books and records of such
     party for the one-year period immediately preceding the date of inspection
     to verify the correctness of the reports given to the other party under
     this Section 6. If a material discrepancy is found in such books and
     records, the right of inspection shall extend to books and records for
     periods prior to such one-year period. Each party shall pay any deficiency,
     plus interest thereon from the date each payment was due, calculated at the
     prime rate of Citibank of New York, within thirty (30) days of the date of
     any notice of such discrepancy. If the deficiency for any year is greater
     than ten percent (10%), the reasonable costs of the audit shall be paid by
     such party. All information learned in the course of any examination of
     each party's books and records hereunder, except when it is necessary to
     reveal such information in order to enforce any rights under this Agreement
     in court, or similar dispute resolution or enforcement proceeding or
     action, shall be treated as confidential information.

7.   PRESS RELEASES AND CONFIDENTIALITY

7.1  Upon executing this Agreement, the parties shall issue a joint press
     release as appearing in Exhibit B.

7.2  Upon entering the permitted ThermoFluor Deal in Infection specified in
     Section 3.3 above, 3DP shall issue a press release which identifies
     Scriptgen as part (i.e., a contributing licensor) of the collaboration
     agreement and states that Scriptgen maintains exclusivity under its
     intellectual property rights regarding future Infection collaborations.

7.3  The parties agree that except as provided in Sections 7.1 and 7.2 above,
     the terms and provisions contained herein shall be confidential. It shall
     not be a breach of this Agreement, however, for any party to: (a) disclose
     this Agreement to its outside counsel, or the financial effect hereof to
     its own accountants, auditors, creditors, investors, potential investors,
     merger partners or potential merger partners, provided that such recipients
     are directed to keep the terms confidential; or (b) make any disclosure
     necessary to comply with the financial, public disclosure or other
     reporting requirements under any applicable laws.

8.  NOTICES

8.1  Under this Agreement, all required notices or communications shall be in
     writing and deemed effective upon receipt if sent by first class mail
     (postage prepaid), courier, or facsimile, and addressed as follows:

                                       7
<PAGE>

     For Scriptgen:      Mark T. Weedon
                         President & CEO
                         Scriptgen Pharmaceuticals, Inc.
                         610 Lincoln Street
                         Waltham, MA 02451
                         Telephone: (781) 768-3400
                         Facsimile: (781) 768-5628

     For 3DP:            David C. U'Prichard, Ph.D.
                         Chief Executive Officer
                         3-Dimensional Pharmaceuticals, Inc.
                         Eagleview Corporate Center
                         665 Stockton Drive, Suite 104
                         Exton, Pa 19341
                         Telephone: (610) 458-8959
                         Facsimile: (610) 458-8258

8.2  The address of either party may be changed by notice duly given to the
     other party.

9.   GENERAL PROVISIONS

9.1  This Agreement is executed voluntarily and without any duress or undue
     influence on the parties or their officers, employees, agents, or
     attorneys. Neither party is relying on any inducements, promises, or
     representations not contained herein made by the other party or any of its
     officers, employees, agents, or attorneys.

9.2  If any legal action or other proceeding is brought to enforce the terms of
     this Agreement, the prevailing party shall be entitled to recover its
     reasonable attorneys' fees and other costs incurred in bringing such action
     or proceeding, in addition to any other relief to which such party may be
     entitled.

9.3  Any provision of this Agreement which is invalid, illegal, or unenforceable
     in any jurisdiction shall, as to that jurisdiction, be ineffective only to
     the extent of such invalidity, illegality, or unenforceability, and shall
     not in any manner affect the remaining provisions hereof in such
     jurisdiction or render any other provision of this Agreement invalid,
     illegal, or unenforceable in any other jurisdiction.

9.4  This Agreement shall be governed by and interpreted in accordance with the
     laws of the State of Delaware, United States of America, without regard to
     the conflict of laws principles thereof.

9.5  The headings used herein are for reference and convenience only, and shall
     not enter into the interpretation of this Agreement. This Agreement
     contains the entire agreement between the parties as to the subject matter
     hereof. This Agreement may not be modified or amended except by a written
     amendment signed by an officer of each party.

                                       8
<PAGE>

9.6  Subject to Sections 3.2 and 5.3, this Agreement shall inure to the benefit
     of and be binding on any and all successors in interest to the parties
     hereto.

9.7  It shall not be a breach of this Agreement for either party to fail to
     perform its obligations under this Agreement on account of any act of God
     or other cause beyond the control of the affected party, subject to such
     party performing such obligation as soon as possible thereafter.

9.8  A breach of any provision of this Agreement may only be waived in writing
     and the waiver of such breach shall not operate or be construed as a waiver
     of any subsequent breach.

9.9  Each party represents and warrants that it has the full and unencumbered
     right, power and authority to enter into this Agreement, to grant the
     license rights granted hereunder, and otherwise to carry out its
     obligations thereunder.

9.10 In making and performing this Agreement, the parties hereto are acting and
     shall act as independent contractors. Neither party is, nor will be deemed
     to be, an agent, legal representative, joint venturer or partner of the
     other party for any purpose. Neither party will be entitled to bind the
     other party without prior written approval, and each party shall bear its
     own expenses and costs in connection with performing its obligations under
     this Agreement.

9.11 This Agreement may be executed originally or by facsimile signature in
     multiple counterparts, each of which shall be deemed an original and all of
     which together shall constitute one instrument, provided however, that this
     Agreement shall not be binding upon either of the parties until such time
     it is actually executed by duly authorized officers of both parties.

IN WITNESS WHEREOF, the parties hereto have caused duplicate originals of this
Settlement Agreement to be executed by their duly authorized officers on the
date(s) set forth below:

Scriptgen Pharmaceuticals, Inc.              3-Dimensional Pharmaceuticals, Inc.

By: /s/ Mark T. Weedon                       By: /s/ David C. U'Prichard
    --------------------------------             -------------------------------
Printed Name: Mark T. Weedon
Title: President & Chief Executive Officer   Printed Name:  David C. U'Prichard
Date: March 7, 2000                          Title:  Chief Executive Officer

                                       9

<PAGE>

                                      10
<PAGE>

                                                                       Exhibit A
                                                                       ---------

                      IN THE UNITED STATES DISTRICT COURT

                          FOR THE DISTRICT OF DELAWARE

SCRIPTGEN PHARMACEUTICALS, INC.,              :

               Plaintiff,                     :

     v.                                       :       C.A. No. 98-583 (GMS)

3-DIMENSIONAL PHARMACEUTICALS, INC.,          :

                                              :

               Defendant.                     :

                         STIPULATED ORDER OF DISMISSAL
                         -----------------------------

     Pursuant to Fed. R.Civ.P. 41(a)(1), it is hereby stipulated by the parties,
subject to the approval of the Court, that this action, including all claims and
counterclaims, is dismissed, with each party to bear its own costs.

                                    POTTER ANDERSON & CORROON LLP

                                    -------------------------------
                                    Richard L. Horwitz (#2246)
                                    Joanne Ceballos (#2854)
                                    Hercules Plaza
                                    P.O. Box 951
                                    Wilmington, Delaware 19899-0951
                                    (302) 984-6000

                                    Attorneys for Plaintiff
                                    Scriptgen Pharmaceuticals, Inc.
<PAGE>

                                    MORRIS, NICHOLS, ARSHT &
                                    TUNNELL

                                    -------------------------------
                                    Jack B. Blumenfeld (#1014)
                                    Julia Heaney (#3052)
                                    1201 N. Market Street
                                    P.O. Box 1347
                                    Wilmington, DE 19899-1347
                                    (302) 658-9200

                                    Attorneys for Defendant
                                    3-Dimensional Pharmaceuticals, Inc.

SO ORDERED this _ day of

__________________, 2000

_____________________________
United States District Judge
<PAGE>

                                                         Exhibit B
                                                         ---------
Contacts:

For Scriptgen:
  Mark T. Weedon                                  Gretchen L.P. Schwaltzer
  Chief Executive Officer                         Feinstein Kean Healthcare
  (781) 768-3400                                  (617) 577-8110

For 3-Dimensional Pharmaceuticals, Inc.
  Michael J. Wassil                               Jerry Parrott
  Chief Financial Officer                         Jerry Parrott & Associates
   (610) 458-6073                                 (212) 472-1244

For Immediate Release
---------------------

                    Scriptgen and 3DP Settle Patent Dispute

        Companies Cross-License High Throughout Screening - Technologies
                           To Advance Drug Discovery

Waltham, Massachusetts, and Exton, Pennsylvania, January XX, 2000 - Scriptgen
Pharmaceuticals, Inc. and 3-Dimensional Pharmaceuticals, Inc. (3DP) announced
today a mutually beneficial settlement of their dispute over Intellectual
property.  3DP has agreed to purchase a limited, non-exclusive worldwide license
to current and pending patents relating to Scriptgen's ATLAS(R) (Any Target
Ligand Affinity Screen) assay technology - a system for identifying compounds
that are drug candidates.  3DP will grant Scriptgen a limited, non-exclusive
worldwide license to pending patents relating to 3DP's ThermoFluor(R) assay
technology.  Under the agreement, both companies can utilize their respective
assay technologies for the identification of novel drugs in a broad range of
therapeutic areas, however, Scriptgen does maintain a preferential position in
the area of anti-infectives.  Financial terms were not disclosed.

Scriptgen Pharmaceuticals, Inc. (http://www.scriptgen.com) is a leader in the
discovery of drugs to control the expression of genes.  Current programs in the
anti-infective area have identified multiple new drug targets and lead compounds
effective against drug-resistant bacterial, fungal and viral pathogens.
Scriptgen's products include GATH, a family of high-throughput target.
Identification and validation technologies and ATLAS and SCAN, high-throughput
screening technologies for proteins and RNA targets, respectively.

3-Dimensional Pharmaceuticals, Inc. is a drug discovery company using
DiscoverWorks(TM), a proprietary technology platform, to reduce the costs and
improve the quality of drugs entering clinical trials.  DiscoverWorks(TM)
uniquely integrates high-throughput screening, combinatorial chemistry and
structure-based drug design for efficient drug discovery using targets from
genome sequencing.  3DP uses DiscoverWorks(TM) in its own drug discovery
programs and to provide discovery services to pharmaceutical and agrochemical
partners.  The company's
<PAGE>

internal research programs are focused on the discovery of orally active small-
molecule pharmaceuticals for the treatment of cardiovascular disease and cancer.
(http://www.3dp.com).<PAGE>

                                                                   Exhibit 10.16

                       RESEARCH COLLABORATION AGREEMENT

     This RESEARCH COLLABORATION AGREEMENT (the "Agreement"), effective as of
October 18, 1996 (the "Effective Date"), is made by and between 3-Dimensional
Pharmaceuticals, Inc. ("3DP"), a Delaware corporation, having a principal place
of business at 665 Stockton Drive, Suite 104, Exton, Pennsylvania 19341, and
BIOCRYST Pharmaceuticals, Inc. ("BIOCRYST"), a Delaware corporation, having a
principal place of business at 2190 Parkway Lake Drive, Birmingham, Alabama
35244.

                                  BACKGROUND

     WHEREAS, 3DP has rights to certain compound libraries and to certain
synthesis and screening technologies (including the DirectedDiversity
technology and the ThermoFluor technology) which, when applied, may reduce the
time and expense of identifying and developing potentially useful compounds for
use in the prevention, treatment, diagnosis and monitoring of diseases, states
and conditions in humans;

     WHEREAS, BIOCRYST has identified certain compounds that are inhibitors of
enzymes or proteins in the Complement System through structure-based drug
design, has conducted extensive research and analysis of the Complement
System, and has certain discoveries, inventions, know-how and technologies
related to the identification, development and optimization of compounds that
are active as inhibitors of the Complement System;

     WHEREAS, subject to the terms and conditions of this Agreement, 3DP
and BIOCRYST desire to have access to each other's technologies, discoveries and
inventions and conduct a joint research program to attempt to identify and
optimize compounds that act as inhibitors of proteins and enzymes in the
Complement System.

     NOW, THEREFORE, for and in consideration of the foregoing premises, and the
covenants, conditions, and undertakings set forth herein, the receipt and
sufficiency of which the parties hereby acknowledge, it is agreed by and between
the parties as follows:

                                   ARTICLE 1
                                  DEFINITIONS

     For purposes of this Agreement the following terms shall have the following
meanings:

     1.1       "3DP Compound" shall mean a compound contained in a 3DP Library
                ------------
and/or any other compound synthesized by 3DP independently of the Research
Program for activity outside the Field excluding BIOCRYST Compounds and any
compound contained in a Focused Library.

     1.2       "3DP Library" shall mean any chemical compound library developed
                -----------
by or on behalf of 3DP independently of the Research Program for activity
outside the Field using the 3DP Technology and excluding Focused Libraries.

     1.3       "3DP Technology" shall mean the patented and proprietary
                --------------
technology developed, licensed or acquired by 3DP prior to the Effective Date or
developed, licensed or acquired by 3DP after the Effective Date either
independently of the Research Program or by 3DP alone without any assistance or
contribution from BIOCRYST as part of the Research Program, which is useful for
the creation of custom combinatorial chemical libraries as well as

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission.  The omitted
portions have been filed separately with the Commission.
<PAGE>

the chemical synthesis of compounds contained in such libraries, including
without limitation the screening technologies known as DirectedDiversity and
ThermoFluor.

     1.4       "Affiliate" shall mean any corporation, firm, partnership or
                ---------
other entity which during the term of this Agreement controls, is directly or
indirectly owned by or controlled by or is under common control with 3DP or
BIOCRYST, respectively, but only for so long as such entity controls, is
directly or indirectly owned by or controlled by, or is under common control
with 3DP or BIOCRYST. For this purpose, control means the possession of the
power to direct or cause the direction of the management and the policies of an
entity whether through ownership, either directly or indirectly, of over fifty
percent (50%) of the stock entitled to vote, or in the case of a non-corporate
entity, the right to receive over fifty percent (50%) of either the profits or
the assets upon dissolution or if not meeting the preceding requirements, any
company owned or controlled by or owning or controlling 3DP or BIOCRYST at the
maximum control or ownership right permitted in the country where such company
exists.

     1.5       "BIOCRYST Compounds" shall mean (i) the compounds and classes of
                ------------------
compounds specified on Exhibit A attached hereto, which have been identified by
                       ---------
BIOCRYST prior to the Effective Date as having activity (or potential activity)
as an inhibitor of enzymes or proteins in the Complement System and (ii) any
derivatives of the compounds specified in  Exhibit A that are
                                           ---------
"obvious" to scientists skilled in the art of compound structure or drug design.
For purposes of this definition, "obvious" shall have the meaning ascribed to
such term by the Federal Patent Laws of the United States of America.

     1.6       "BIOCRYST Compound Derivative" shall mean a compound that (i)
                ----------------------------
has been synthesized in the course of the Research Program and demonstrates
activity within the Field, (ii) is not a BIOCRYST Compound but (iii) is a non-
obvious derivative of a BIOCRYST Compound. For purposes of this definition,
"obvious" shall have the meaning ascribed to such term by the Federal Patent
Laws of the United States of America.

     1.7       "BIOCRYST Technology" shall mean BIOCRYST's structure based drug
                -------------------
design technologies developed, licensed or acquired by BIOCRYST prior to the
Effective Date or developed, licensed or acquired by BIOCRYST after the
Effective Date either independently of the Research Program or by BIOCRYST alone
without any assistance or contribution from 3DP as part of the Research Program.

     1.8       "Complement System" shall mean the system of plasma proteins
                -----------------
that work to eliminate microorganisms and other antigens from tissues and
blood. This task is achieved either by complement components alone or by
complement components in conjunction with antibodies and/or cells that express
complement receptors.

     1.9       "Confidential Information" means all non-public, proprietary or
                ------------------------
otherwise confidential information, now owned, licensed or controlled or
hereafter acquired, developed, owned, licensed or controlled by a disclosing
party or any of its Affiliates during the Term of this Agreement. Confidential
Information shall include, but not be limited to: (i) BIOCRYST Compounds and
BIOCRYST Technology; (ii) the 3DP Libraries, the 3DP Compounds and the 3DP
Technology; (iii) Focused Libraries and Research Results; (iv) Lead Compounds,
BIOCRYST Compound Derivatives, Optimized Lead Compounds, and Development
Candidates; and (v) Products prior to their first commercial sale.

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission.  The omitted
portions have been filed separately with the Commission.

                                       2
<PAGE>

     1.10      "Consultant" shall mean any Third Party that has been retained by
                ----------
either party to assist such party in performing any of its research obligations
under this Agreement, and, in the case of BIOCRYST, includes, without
limitation, the University of Alabama at Birmingham.

     1.11      "Development Candidate" shall mean a Lead Compound, BIOCRYST
                ---------------------
Compound Derivative or an Optimized Lead Compound identified in the course of
the Research Program that meets the criteria for full preclinical development of
such compound into a drug for human use (i) as set forth in the Research Plan or
(ii) as otherwise agreed by the parties.

     1.12      "Field" shall mean inhibitors of the Complement System enzymes
                -----
and proteins specified in Exhibit B attached hereto, and all uses and
applications thereof; provided, however, that the Field may be broadened to
                      --------  -------
include other Complement System enzymes and proteins by mutual agreement of
both parties in writing.

     1.13      "Focused Assay" shall mean a test or trial developed specifically
                -------------
for screening against Focused Libraries in the course of the Research Program,
to identify Lead Compounds, BIOCRYST Compound Derivatives or Optimized Lead
Compounds that have activity in the Field, including, without limitation,
ThermoFluor technology.

     1.14      "Focused Library" shall mean any chemical compound library that
                ---------------
has been synthesized by or on behalf of 3DP specifically for use by or on behalf
of 3DP or BIOCRYST in the course of the Research Program.

     1.15      "Interest" shall mean a party's right, title and interest in any
                --------
Jointly Owned Right.

     1.16      "Invention" shall mean any invention or discovery, whether or not
                ---------
patented or patentable, including, but not limited to, discoveries,
compositions, know-how, procedures, technical information, and any process,
method, device, formula, protocol, technique, design, drawing, methodology, and
biological or chemical material.

     1.17      "Jointly Owned Rights" shall have the meaning ascribed to such
                --------------------
term in Section 5.2 hereto.

     1.18      "Lead Compound" shall mean a chemically defined compound that
                -------------
has been synthesized in the course of the Research Program, has activity in the
Field and which meets the criteria set forth in the Research Plan to be fit for
optimization, but excluding BIOCRYST Compounds and BIOCRYST Compound
Derivatives.

     1.19      "License Income" shall mean the gross amount actually received by
                --------------
either party or its Affiliates for or on account of authorized licenses of
rights to any Development Candidate or any Product containing such Development
Candidate, including upfront license fees, milestone payments and royalties (the
amount of the gross royalties being determined by the terms of the agreement
with the authorized licensee, which may take into account factors such as
combination sales) without deduction of any kind, but excluding the following:

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission.  The omitted
portions have been filed separately with the Commission.

                                       3
<PAGE>

               (a)  Payments received by either party or its Affiliate solely
          for performance of research and development, including but not limited
          to milestone payments for achievement of objectives in research and
          development, only to the extent that such payments cover the actual
          cost of the research and development work.

               (b)  Investments made by a licensee in either party or its
          Affiliates to the extent that such investments are made at current
          market value, including but not limited to, any payments or other
          consideration representing the current market value of shares in such
          party or its Affiliates.

               (c)  Payments made to either party or its Affiliate solely to the
          extent that they cover the actual costs of conducting clinical testing
          and other activities in connection with obtaining regulatory approval
          for a Product.

               (d)  Reimbursed expenses of either party or its Affiliates.

          For purposes of Subparagraph (b) above, the "current market value" of
the investment shall be determined as follows: (i) it shall be determined as at
the earlier of (a) the date when the investment is made or (b) the day prior to
the date when the investment is first publicly disclosed on the Dow Jones News
                                                                --------------
Wire (the "Determination Date"); (ii) if there is no public market for the
----
party's securities that are being purchased by the licensee, then the current
market value shall be determined by that party's Board of Directors in good
faith, and if the other party disputes such determination, the current market
value shall be determined by an independent investment banker whose fees shall
be shared by the parties; (iii) if there is a public market for such party's
securities that are being purchased by the licensee, then the current market
value shall be determined using the average of the closing price quoted on any
exchange on which the securities are listed as published in The Wall Street
                                                            ---------------
Journal for the ten (10) trading days prior to the Determination Date.
-------
Notwithstanding the foregoing, in the event the licensee is purchasing a party's
securities in connection with such party's initial public offering of such
securities, the current market value shall be determined using the offering
price of such securities to the public in such party's initial public offering.
                                                                              -

     1.20 "Net Sales" shall mean the gross invoice price of a Product sold by
           ---------
3DP, BIOCRYST or their Affiliates ("Selling Party") to Third Parties, less, to
the extent included in such invoice price, the total of: (i) ordinary and
customary trade discounts actually allowed; (ii) credits, rebates and returns;
(iii) freight, postage, and duties paid for and separately identified on the
invoice or other documentation maintained in the ordinary course of business;
and (iv) excise taxes, sales taxes, value added taxes, and duties actually paid
and separately identified on the invoice or other documentation maintained in
the ordinary course of business. Net Sales shall also include the amount or fair
market value of all other considerations received by the Selling Party from
Third Parties in respect of a Product, whether such consideration is in cash,
payment in kind, exchange, or another form. Sales between or among 3DP or
BIOCRYST and their respective Affiliates or authorized licensees shall be
excluded from the computation of Net Sales, except where such Affiliates or
authorized licensees are end users of the Product, in which case such sales
shall be deemed to have been made for cash at a price equal to the amount that
would

                                       4
<PAGE>

be charged to a Third Party at such time, in an arms-length transaction for a
similar quantity of the Product. A "sale" of a Product is deemed to occur upon
the earlier of invoicing, shipment or transfer of title in the Product to a
Third Party, unless a party's Affiliate or licensee is an end user of the
Product, in which case the sale shall occur upon the transfer of the Product to
the Affiliate or licensee that is the end user. In the event that a Product is
sold or distributed for use in combination with or as a component of other
products, the calculation of "Net Sales" from such combination product shall be
determined (i) by agreement of the parties acting reasonably in good faith or
(ii) if agreement cannot be reached within six (6) months after commencement of
negotiations, by arbitration in accordance with Article 10 hereof, in either
case considering the relative importance and proprietary protection of the
various products and components involved.

     1.21      "Optimized Lead Compound" shall mean a Lead Compound or a
                -----------------------
BIOCRYST Compound Derivative which, through a process of optimization,
demonstrates a specified level of activity in the Field (i) as set forth in the
Research Plan or (ii) as otherwise agreed by the parties.

     1.22      "Patent Rights" shall mean patent applications and issued
                -------------
patents, in the United States or any other country or jurisdiction, as well as
any divisions, continuations, continuations-in-part, reissues, reexaminations,
patents of addition, extensions or other governmental actions which extend any
of the subject matter of such patent application or patent, and any
substitutions, confirmations, registrations, or revalidation of any of the
foregoing.

     1.23      "Product" shall mean any product containing a Development
                -------
Candidate.

     1.24      "Proprietary Rights" shall mean Patent Rights, copyrights, trade
                ------------------
secret rights, trademarks and similar rights.

     1.25      "Research Committee" or "RC" shall mean the research organization
                ------------------      --
comprising representatives of 3DP and BIOCRYST as described in Article 3 hereof.

     1.26      "Research Plan" shall mean the written overall plan prepared by
                -------------
the RC for the Research Program the parties will conduct in the Field during the
Term.

     1.27      "Research Program" shall mean the program of collaborative
                ----------------
research in the Field to be carried out by the parties in accordance with the
Research Plan and the terms and conditions of this Agreement.

     1.28      "Research Program Invention" shall mean an Invention first
                --------------------------
conceived, identified, isolated, created or first reduced to practice by the
parties, either independently or jointly, in the course of the Research Program
excluding any improvement to 3DP's DirectedDiversity, BIOCRYST Technology and
either party's assay technologies.

     1.29      "Research Results" shall mean all data and information arising
                ----------------
from either party's performance of its obligations under the Research Plan in
the course of the Research Program.

                                       5
<PAGE>

     1.30      "Term" shall mean the period commencing on the Effective Date and
                ----
terminating in accordance with Article II hereof.

     1.31      "Third Party" shall mean any person, business or entity other
                -----------
than 3DP, BIOCRYST, and their respective Affiliates.

     1.32      "Third Party Obligation" shall mean any contractual or other
                ----------------------
obligation of a party or any of its Affiliates to a Third Party, including,
without limitation, an obligation to make payments to a Third Party for a
license to technology or in respect of a Third Party's Proprietary Rights.

     1.33      "Unresolved Dispute" shall mean a dispute or disagreement that
                ------------------
has arisen between the parties in connection with the validity, construction,
meaning, enforceability, or performance of this Agreement or in connection with
any aspect of the arrangements under this Agreement, that has been submitted for
resolution to the RC, and to the senior officers of each party in accordance
with Section 3.4 hereof, and remains unresolved after taking such steps.

                                   ARTICLE 2
                        COLLABORATIVE RESEARCH PROGRAM

     2.1       Preparation of Research Plan.  Promptly after execution of this
               -----------------------------
Agreement, the parties' representatives on the RC shall commence preparation of
a detailed research plan which shall set forth the parties' respective
obligations and responsibilities in connection with the Research Program. Once
the RC has prepared the proposed research plan, it shall submit the proposed
research plan to the appropriate members of management of both parties for their
review. Once the parties mutually agree that the proposed research plan is in an
acceptable form, the proposed research plan shall become the Research Plan for
purposes of this Agreement once it has been executed and delivered by a duly
authorized representative of each party.

     2.2       Research Program Activities.  Once the Research Plan has been
               ----------------------------
completed and executed and delivered, subject to the terms and conditions set
forth herein, the parties shall carry out the Research Program in accordance
with the Research Plan with the goal of identifying Lead Compounds and Optimized
Lead Compounds. The RC shall review the Research Plan on an ongoing basis and
may revise the Research Plan periodically or as necessary by agreement of the RC
in accordance with Article 3 hereto.

               2.2.1     BIOCRYST's Responsibilities.  BIOCRYST shall have the
                         ---------------------------
following responsibilities, which shall be carried out in accordance with the
Research Plan in the Field:

                         (a)  providing results of its research, structural
               knowledge of compounds and information regarding Research
               Program Inventions, all within the Field;

                         (b)  through its participation in the RC, designing
               Lead Compounds based in part on the structural knowledge,
               discoveries, Research Program Inventions, research results and
               expertise described in Section 2.2.1(a) above;

                                       6
<PAGE>

                         (c)  conducting optimization of Lead Compounds or
               BIOCRYST Compound Derivatives either independently or jointly
               with 3DP;

                         (d)  conducting preliminary preclinical
               pharmacological analyses of Lead Compounds and Optimized Lead
               Compounds to evaluate potency, efficacy and selectivity;

                         (e)  presenting Lead Compounds, Optimized Lead
               Compounds and the Research Results in relation thereto to the RC;

                         (f)  providing adequate reagents for screening;

                         (g)  screening assays as appropriate to validate and
               confirm Focused Assay results; and

                         (h)  performing such other responsibilities set forth
               in this Agreement or that the parties may mutually agree upon
               in writing.

               2.2.2     3DP's Responsibilities. 3DP shall have the following
                         -----------------------
responsibilities, which shall be carried out in accordance with the Research
Plan in the Field:

                         (a)  preparing Focused Libraries;

                         (b)  preparing Focused Assays;

                         (c)  screening the Focused Libraries using the Focused
               Assays of its DirectedDiversity technology and ThermoFluor
               technology, conducting chemical synthesis of the compounds in
               the Focused Library which have activity in the Field discovered
               by such screening, identifying Lead Compounds and providing
               Research Results in relation thereto to the RC;

                         (d)  conducting optimization of Lead Compounds or
               BIOCRYST Compound Derivatives either independently or jointly
               with BIOCRYST;

                         (e)  presenting Lead Compounds, Optimized Lead
               Compounds and Research Results in relation thereto to the RC; and

                         (f)  performing such other responsibilities set forth
               in this Agreement or that the parties may mutually agree upon in
               writing.

               2.2.3     Research Licenses.  Subject to all the terms and
                         ------------------
conditions of this Agreement, and only to the limited extent necessary for the
purposes of this Agreement, each party (the "Licensor") hereby grants to the
other party (the "Licensee") under its Proprietary Rights, a royalty free, non-
transferable, non-sublicensable, license to conduct the Licensee's research
responsibilities under the Research Plan for the Term of this Agreement.

                                       7
<PAGE>

               2.2.4     Disclosure of Research Results and Research Program
                         ---------------------------------------------------
Inventions. Each party shall promptly disclose in writing to the chief
----------
scientific officer of the other party and to the RC, all Research Results and
Research Program Inventions it develops, conceives or first reduces to practice
in the course of the Research Program.

     2.3  Access to Focused Libraries and Screening.  BIOCRYST shall have direct
          ------------------------------------------
access to the Focused Libraries during the Research Program, as is necessary for
purposes of the Research Program.

     2.4  BIOCRYST Compounds and BIOCRYST Technology.  3DP acknowledges that (i)
          --------------------------------------------
BIOCRYST has previously expended substantial financial and research resources in
relation to its work in the Field and the BIOCRYST Technology that exists as of
the Effective Date, (ii) has identified the BIOCRYST Compounds and (iii) has an
on-going research, development and commercialization program in relation to the
BIOCRYST Compounds in the Field which BIOCRYST shall be conducting independently
of the arrangements under this Agreement. Notwithstanding any other provision of
this Agreement to the contrary, the parties agree that BIOCRYST shall be free to
(a) conduct its independent research, development and commercialization program
in the Field in relation to BIOCRYST Compounds using the BIOCRYST Technology,
(b) research, develop and commercialize BIOCRYST Compounds and any product or
service based thereon in the Field, without restriction, reference or payment to
3DP, (c) conduct any independent research, development and commercialization
program outside the Field in relation to BIOCRYST Compounds and BIOCRYST
Technology and (d) research, develop and commercialize BIOCRYST Compounds,
BIOCRYST Technology and any product or service based thereon outside the Field,
without restriction, reference or payment to 3DP.

     2.5  3DP Compounds, 3DP Libraries and 3DP Technology.  BIOCRYST
          -------------------------------------------------
acknowledges that 3DP (i) has previously expended substantial financial and
research resources in relation to the 3DP Compounds, the 3DP Libraries and the
3DP Technology that exist as of the Effective Date and (ii) has an on-going
research, development and commercialization program in relation to the 3DP
Compounds, the 3DP Libraries and the 3DP Technology outside the Field which 3DP
shall be conducting independently of the arrangements under this Agreement.
Notwithstanding any other provision of this Agreement to the contrary, the
parties agree that 3DP shall be free to (a) conduct its independent research,
development and commercialization program outside the Field in relation to the
3DP Compounds, the 3DP Libraries and the 3DP Technology, (b) research, develop
and commercialize such 3DP Compounds, 3DP Libraries, the 3DP Technology and any
product or service based thereon outside the Field, without restriction,
reference or payment to BIOCRYST and (c) test within the Field any 3DP Compounds
which have activity outside the Field solely to establish the potential for
side-effects.

     2.6  Records.  3DP, BIOCRYST and their Affiliates shall maintain records of
          --------
their own activities and conduct in the course of the Research Program (or cause
such records to be maintained) in sufficient detail and in good scientific
manner as will properly reflect all work done and results achieved in the
performance of the Research Program (including, but not limited to, all data in
the form required under any applicable governmental regulations and as

                                       8
<PAGE>

directed by the RC). Each party shall allow the other party, at the other
party's sole cost, to have reasonable access to all pertinent materials and data
generated by or on behalf of such party in connection with the Research Program.

     2.7  Expenditures.
          -------------

          2.7.1     BIOCRYST Expenditures.  BIOCRYST shall bear all costs and
                    ----------------------
expenses (other than 3DP's costs of participating in the RC and reviewing the
Research Results from BIOCRYST's work) related to (i) performance of its
obligations under Section 2.2.1 hereof and (ii) performance of all its other
obligations under the Research Plan.

          2.7.2     3DP Expenditures.  3DP shall bear all costs and expenses
                    -----------------
(other than BIOCRYST's costs of participating in the RC and reviewing the
Research Results from 3DP's work) related to (i) performance of its obligations
under Section 2.2.2 hereof and (ii) performance of all its other obligations
under the Research Plan.

          2.7.3     Third Party Obligations.  Each party shall be responsible
                    ------------------------
for its own Third Party Obligations in connection with the Research Program,
this Agreement and any further development and commercialization of a
Development Candidate and any Product containing such Development Candidate. In
the event that it is necessary for either party to acquire any new Third Party
Obligations (i.e., a Third Party Obligation not existing as of the Effective
             ----
Date) for the conduct of its duties and obligations under the Research Program,
the party acquiring such license shall be solely responsible for such Third
Party Obligations, unless the parties mutually agree in writing to alternative
arrangements.

          2.7.4     After determination of a Development Candidate. After the
                    -----------------------------------------------
date on which the RC determines that an Optimized Lead Compound is a Development
Candidate, the parties shall no longer be responsible individually for
expenditures in relation to such Development Candidate. All such post-
determination expenditures shall be borne in accordance with the arrangements
set forth in Sections 2.9 and 2.10 hereof and any other arrangements the parties
mutually agree upon in writing.

     2.8  Development Candidates.
          ----------------------

          2.8.1     Determination of Development Candidates. The RC shall have
                    ---------------------------------------
responsibility for determining if an Optimized Lead Compound meets the criteria
specified in the Research Plan for a Development Candidate. If the RC determines
that an Optimized Lead Compound is a Development Candidate, it shall promptly
give written notice of its decision to each of the parties (a "Development
Candidate Notice"). The RC shall also prepare a written report of the Research
Results in relation to such Development Candidate and deliver a copy of such
report to each of the parties as soon as possible after giving each party the
Development Candidate Notice.

          2.8.2     Joint Notice.  Provided that a Development Candidate Notice
                    -------------
and Research Results report have been delivered to each party in accordance with
Section 2.8.1 hereof, if within sixty (60) days of the date of the determination
of a Development Candidate by

                                       9
<PAGE>

the RC each party gives written notice to the other that it desires to fund
development and commercialization of the Development Candidate, the parties
shall promptly after receipt of the later of the two notices enter into good
faith negotiations in accordance with Section 2.9 hereof.

          2.8.3     Single Notice.  Provided that a Development Candidate
                    --------------
Notice and Research Results report have been delivered to each party in
accordance with Section 2.8.1 hereof, if within sixty (60) days of the date of
the determination of a Development Candidate by the RC, only one party (the
"Electing Party") gives written notice to the other that it desires to fund
development and commercialization of the Development Candidate, the Electing
Party shall have exclusive rights to develop and commercialize the Development
Candidate at its sole expense in accordance with Section 2.10 hereof.

     2.9  Joint Development and Commercialization.  In the event that both
          ----------------------------------------
parties elect to develop and commercialize a Development Candidate in accordance
with Section 2.8.2 hereof, the parties shall promptly, after such election,
begin good faith negotiations as to the arrangements and terms and conditions
for further development and commercialization of such Development Candidate,
including without limitation, the following:

          2.9.1     Funding Commitments.  The parties shall determine the
                    --------------------
funding commitments and arrangements for the development and commercialization
of each Development Candidate. Such funding commitments and arrangements shall
include, without limitation, the cost of providing research scientists,
administration and management staff, research facilities, animal studies,
clinical trials, and manufacturing. The parties shall also determine a written
budget for the short term funding commitments. If the parties agree to share
equally the funding commitments for the development and commercialization of the
Development Candidate, the parties shall also share equally in any income from
the commercialization of any resulting products or services. If the parties
agree to unequal funding commitments for the development and commercialization
of such Development Candidate, any income from resulting products or services
shall be shared in proportion to the funding commitments made by the parties.
The funding commitments and arrangements, reallocation of interests in a
Development Candidate in the event of failure to meet funding commitments and
the arrangements for sharing of income from the commercialization of any Product
containing the Development Candidate shall be dealt with in a written agreement
between the parties (a "Development and Commercialization Agreement").

          2.9.2     Development.  The Development and Commercialization
                    ------------
Agreement shall also identify the party or parties and/or any Third Parties that
shall be responsible for carrying out the development and commercialization of
the Development Candidate into a Product.

          2.9.3     Licenses.  The Development and Commercialization Agreement
                    ---------
shall also specify the terms of the grant of any necessary licenses or
assignments of rights to the Development Candidate, Research Results, and
Proprietary Rights in relation thereto.

          2.9.4     Third parties.  BIOCRYST and 3DP may also consider
                    --------------
reasonable proposals for development and commercialization of the Development
Candidate by one or more Third Parties, with or without any participation by
BIOCRYST and/or 3DP.

                                       10
<PAGE>

     2.10 Independent Development and Commercialization.  The parties agree that
          ----------------------------------------------
a party shall be an "Independently Developing Party" in respect of a Development
Candidate if (i) such party is the Electing Party pursuant to Section 2.8.3
hereof, (ii) the parties agree in writing that such party will be solely
responsible for the future funding of the development and commercialization of a
Development Candidate, or (iii) the other party has paid less than its agreed
share of the funding for the development and commercialization of the
Development Candidate for a period in excess of six (6) months. If a party
becomes an Independently Developing Party, the other party shall thereafter be
referred to as the "Non-Developing Party" in respect of such Development
Candidate. Each party agrees that if the other party becomes an Independently
Developing Party, it, as the Non-Developing Party with respect to such
Development Candidate, shall and hereby does grant the Independently Developing
Party, in respect of the subject Development Candidate and limited to the Field,
an exclusive, worldwide, fully sublicensable, irrevocable license, under all of
its Proprietary Rights relating in any way to the Development Candidate and any
Product containing the Development Candidate, to develop, improve, modify, make,
have made, use and sell the Development Candidate and any Product containing the
Development Candidate, subject to the terms and conditions of this Agreement.
The Independently Developing Party shall indemnify, defend and hold harmless the
Non-Developing Party and its employees and agents (the "Non-Developing Party
Indemnitee"), against any and all causes of action, liability, damage, loss or
expense (including, but not limited to, reasonable fees and disbursements of
counsel incurred by the Non-Developing Party Indemnitee in any action or
proceeding between the Independently Developing Party and the Non-Developing
Party Indemnitee or between the Non-Developing Indemnitee and any third party or
otherwise) arising from (a) any product liability or other lawsuit, claim,
demand or other action brought with respect to the subject Development Candidate
or any Product based thereon, or (b) the death of or injury to any person or
persons, damage to property, or any other claim, proceeding, demand, expense and
liability of any kind whatsoever resulting from the design, testing (including,
without limitation, clinical trials), production, manufacture, shipping,
handling, use (in commerce or otherwise), sale, lease, consumption, promotion or
advertisement of the subject Development Candidate or any Product based thereon.
The foregoing indemnity shall be subject to the procedures set forth in Section
9.3 hereof.  The parties also agree to negotiate in good faith as to any other
terms and conditions as are necessary in relation to the independent development
of a Development Candidate by an Independently Developing Party. If the Non-
Developing Party has made no or nominal funding payments for the development and
commercialization of the subject Development Candidate, the Minimum Royalty as
described in Section 2.11 hereto shall be the only payment due to the Non-
Developing Party for the subject Development Candidate, the license granted to
the Independently Developing Party in respect of the Development Candidate under
this Section 2.10, and the Non-Developing Party's contribution to the
identification and optimization of the Development Candidate as part of the
Research Program. In the event that the Non-Developing Party has made some
funding payments in respect of the Development Candidate, the Non-Developing
Party shall be entitled to the payments specified by the applicable Development
and Commercialization Agreement, which shall not be less than the Minimum
Royalty unless the parties otherwise agree in writing.

     2.11 Minimum Royalty for Non-Developing Party.  Unless the parties
          -----------------------------------------
otherwise agree in writing, a Non-Developing Party shall be entitled to a
minimum payment in respect of the subject Development Candidate and any
Product containing such Development Candidate, on a country-by-country basis,
equal to [**] of the Net Sales of such Product by the Independently Developing
Party and its Affiliates in the particular country and/or [**] of License
Income received by the Independently Developing Party and its Affiliates in
relation to such Development Candidate and any Product containing such
Development Candidate in the particular country; provided that such payments
shall only be due if, at the time of the sale, the Development Candidate or
Product is claimed in (i) a pending claim contained in a patent application in
such country, or (ii) a valid and unexpired claim contained in a patent in
such country (the "Minimum Royalty").

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission.  The omitted
portions have been filed separately with the Commission.

                                       11
<PAGE>

                                   ARTICLE 3
                                  MANAGEMENT

     3.1  Research Committee.  The parties shall establish a Research Committee
          ------------------
("RC") which shall be in existence for the Term of this Agreement, to oversee,
review and coordinate the conduct of the Research Program.  The responsibilities
of the RC shall include without limitation:

          3.1.1     drafting the Research Plan promptly after the execution of
                    this Agreement;

          3.1.2     determining the research and manpower commitments to be
                    made by the parties pursuant to the Research Plan;

          3.1.3     determining criteria for Lead Compounds, Optimized Lead
                    Compounds and Development Candidates;

          3.1.4     reviewing the Research Results, choosing Lead Compounds for
                    optimization and reporting research progress towards the
                    Research Program's objectives to each of the parties;

          3.1.5     ensuring open and frequent exchange between both parties of
                    biological, chemical, screening and other technological
                    advances and Research Program Inventions;

          3.1.6     reviewing the Research Program's objectives, and proposing
                    appropriate changes to the Research Plan as necessary;

          3.1.7     reviewing all patent applications for Research Program
                    Inventions and coordinating all other patent related
                    activities resulting from the Research Program in
                    accordance with the terms of this Agreement; and

          3.1.8     taking such other actions as the parties may mutually
                    agree, from time to time, during the Term of this Agreement.

     3.2  Membership of Research Committee.  The RC shall be comprised of three
          --------------------------------
representatives from each of 3DP and BIOCRYST.  Each party's representatives
shall be selected solely by that party, but must be appropriately technically
qualified.  The initial representatives of each party on the RC are listed on
Exhibit C attached hereto.  3DP and BIOCRYST may replace their respective RC
---------
representatives at any time, upon written notice to the other party.  The RC
shall be chaired as agreed by the members of the RC.  From time to time, the RC
may establish subcommittees to oversee particular projects or activities, and
such subcommittees will be constituted as the RC agrees.

     3.3  RC Meetings.  During the Term of this Agreement, the RC shall meet at
          -----------
least four (4) times per year either in person or by telephone or video
conference, at regular intervals, or more often as agreed by the parties, at
alternate or such other mutually agreed locations and times as the parties
agree.  With the consent of the parties, other representatives of 3DP or

                                       12
<PAGE>

BIOCRYST or their Affiliates may attend RC meetings as non-voting observers.
Each party shall be responsible for all of its own expenses in connection with
the RC, including without limitation, compensation, if any, for its
representatives to the RC.

     3.4  Decision Making.  Each party shall be entitled to one vote
          ---------------
irrespective of the actual number of each such party's representatives on the RC
present at the relevant RC meeting, provided, however, that at least one (1)
                                    --------  -------
representative of each party is present at such meeting.  In the event that a
decision is not achieved within the RC, the dispute will be referred to 3DP's
Chief Scientific Officer (or designee of similar rank) and BIOCRYST's Chief
Scientific Officer (or designee of similar rank), who shall promptly meet and
endeavor to resolve the dispute in a timely manner. In the event such
individuals are unable to resolve such dispute, the matter shall be referred to
the respective Chief Executive Officers ("CEOs") of 3DP and BIOCRYST, who shall
promptly meet and endeavor to resolve the dispute. In the event that the
respective CEOs of 3DP and BIOCRYST are unable to resolve such dispute, the
dispute shall be deemed an "Unresolved Dispute" and shall be submitted to
binding arbitration decision in accordance with Article 10 hereof.

     3.5  Reports.  Within twenty (20) days following each RC meeting during the
          -------
Term of this Agreement, the RC shall prepare and provide to each party a
reasonably detailed written summary report which shall (i) summarize all matters
discussed by the RC, (ii) state any determinations of the RC regarding any
matters discussed by the RC described in clause (i) above including, but not
limited to, any determinations regarding any Lead Compounds, Optimized Lead
Compounds, Development Candidates, Research Results, and Patent Rights and (iii)
summarize the reasons for each determination described in clause (ii) above.

                                   ARTICLE 4

                                  EXCLUSIVITY

     4.1  3DP's Exclusivity Commitment.  3DP agrees that during the Term of this
          -----------------------------
Agreement, it shall conduct research within the Field only with BIOCRYST and as
part of the Research Program.  3DP further agrees that, during the Term of this
Agreement, other than in the course of the Research Program, it shall not (i)
knowingly design, develop, use, make or synthesize compounds or chemical
compound libraries for itself, any Affiliate or any Third Party specifically for
screening within the Field or (ii) perform screening or DirectedDiversity? or
ThermoFluor? for itself, any Affiliate or any Third Party within the Field.
Notwithstanding any of the foregoing, testing solely to establish the potential
for side effects of 3DP Compounds that have activity outside the Field will not
be deemed to constitute screening within the Field.

     4.2  BIOCRYST's Exclusivity Commitment.  Except in relation to BIOCRYST
          ----------------------------------
Compounds, BIOCRYST agrees that during the Term of this Agreement it shall
conduct research within the Field only with 3DP and as part of the Research
Program.

     4.3  Use of Consultants.  Nothing in this Agreement shall be construed as
          -------------------
restricting either party's right to conduct research within the Field with any
Consultant in furtherance of the Research Program; provided, however, that such
                                                   --------  -------
party shall require each Consultant to sign (i) a non-disclosure agreement the
provisions of which shall be substantially similar to those of Article 7 of this
Agreement and (ii) an agreement which provides for the assignment of all

                                       13
<PAGE>

Proprietary Rights to the Consultants' work product and Inventions made for the
hiring party, to the hiring party (who is in turn subject to the ownership
provisions contained herein).  Unless 3DP and BIOCRYST otherwise agree in
writing, Consultants shall not participate in the commercialization of any
Development Candidate or Product.

                                   ARTICLE 5

                                   OWNERSHIP

     5.1  Retained Rights.  The parties agree that they shall each separately
          ----------------
retain all their respective rights, title and interest in relation to any
Invention, technology, know-how, compound, product, process, information or
Proprietary Right which they either (i) held prior to the Effective Date or (ii)
they conceive, identify, isolate' create, first reduce to practice, license or
acquire entirely independently of the Research Program (which shall be subject
to reasonable documented verification). Nothing contained herein shall be deemed
to create a license or right under any of the foregoing for purposes outside the
scope of the Research Program, including without limitation, the development and
commercialization of Development Candidates. The parties specifically agree
that, subject to the licenses granted herein, (i) BIOCRYST shall retain all
right, title and interest (including, but not limited to, any Proprietary
Rights) that BIOCRYST holds in relation to BIOCRYST Compounds and BIOCRYST
Technology and (ii) 3DP shall retain all right, title and interest (including,
but not limited to, any Proprietary Rights) that 3DP holds in relation to the
3DP Compounds, 3DP Libraries and 3DP Technology. The Focused Libraries will not
include any 3DP Compounds. In the event that 3DP desires to include a 3DP
Compound in a Focused Library, 3DP shall give prior written notice to BIOCRYST
of its intention and the parties shall negotiate in good faith as to the terms
and conditions for use of such 3DP Compound in the course of the Research
Program. In the event no such prior notice is given, any compound contained
within a Focused Library may not thereafter qualify as a 3DP Compound for
purposes of this Agreement. Notwithstanding the foregoing, 3DP shall retain full
right, title and interest in any 3DP Compounds that have activity outside the
Field which have been tested within the Field solely to establish the potential
of side-effects.

     5.2  Ownership of Result from the Research Program.  3DP and BIOCRYST shall
          ----------------------------------------------
jointly own in equal shares all right, title and interest to any Lead Compounds,
Optimized Lead Compounds, BIOCRYST Compound Derivatives, Research Results,
Research Program Inventions or any other results from the Research Program
(including, but not limited to, the utility of the foregoing both within and
outside the Field) that may be conceived, identified, isolated, created or first
reduced to practice by the parties, either independently (subject to Sections
1.3 and 1.7 hereof) or jointly, during the Term of this Agreement or within
twelve (12) months of the effective date of termination or expiration of this
Agreement; provided, however, that the foregoing shall not apply to any
compounds that might have utility outside the Field and that have not been
synthesized during the course of the Research Program ("Jointly Owned Rights").

     5.3  Ownership of Proprietary Rights resulting from the Research Program.
          --------------------------------------------------------------------
3DP and BIOCRYST shall also jointly own in equal shares all right, title and
interest to any and all Proprietary Rights that arise in relation to any Jointly
Owned Rights. Each party hereby represents that all employees and other persons
acting on its behalf in performing its obligations

                                       14
<PAGE>

under this Agreement shall be obligated under a binding written agreement to
assign to such party, or as such party shall direct, all Lead Compounds,
Optimized Lead Compounds, BIOCRYST Compound Derivatives, Research Program
Inventions and Research Results made or developed by such employees or other
persons.

     5.4  Assignment.  The parties hereby make any assignments necessary to
          ----------
accomplish the joint ownership provisions set forth in Sections 5.2 and 5.3
hereof. A party being assigned any Proprietary Right or any interest therein
under this Agreement will have the right, at such party's expense, to require
that the assigning party assist such party in every proper way (including,
without limitation, becoming a nominal party) to evidence, record and perfect
the assignment and to apply for and obtain recordation of and from time to time
enforce, maintain, and defend such Proprietary Right.

     5.5  Buyout.  Either party may initiate, at any time during the Term or at
          -------
any stage during the development and commercialization of any Development
Candidates, discussions to buy out the other party's Interest, or to sell its
own Interest, to the other, or to sell both parties' Interests to a Third Party.
In the event either party initiates such discussions, both parties will
negotiate such a buyout or sale, as the case may be, in good faith; provided,
however, that neither party will be obligated to sell or buy any such Interest.

     5.6  Commercialization of Jointly Owned Rights.  Except as set forth in
          -------------------------------------------
Section 2.9 hereof and for the purposes of the Research Plan, neither 3DP nor
BIOCRYST shall have the right to use or commercialize any Jointly Owned Right or
any Proprietary Rights in relation thereto, either inside the Field or outside
the Field, during the Term of this Agreement or at any time thereafter, without
the prior written consent or agreement of the other party.

                                   ARTICLE 6

                      PATENT PROSECUTION AND ENFORCEMENT

     6.1  Prosecution.  The RC shall determine, from time to time, the party or
          ------------
parties that (i) shall be responsible for preparing, filing, prosecuting and
maintaining in such countries the RC deems appropriate, patent applications and
patents relating to Research Program Inventions, (ii) shall be responsible for
conducting any interferences, reexaminations, reissues and oppositions relating
to such Research Program Inventions. The parties shall bear in equal shares the
costs arising under this Section 6. 1.

     6.2  Cooperation.  Each of BIOCRYST and 3DP shall keep the other fully
          -----------
informed as to the status of patent matters described in this Article 6,
including without limitation, by providing the other the opportunity to fully
review and comment on any substantive documents (i.e., documents affecting the
                                                 ----
scope of the Research Program Invention) which will be filed in any patent
office as far in advance of filing dates as practicable, and providing the other
with copies of any substantive documents that such party receives from such
patent offices promptly after receipt, including notice of all interferences,
reissues, re-examinations, oppositions or requests for patent term extensions.
Upon request by BIOCRYST and 3DP, the other party shall provide copies of any
patent documents in addition to those described in the preceding sentence.
BIOCRYST and 3DP shall each reasonably cooperate with and assist the other in
connection with such activities, at the other party's request. Patent counsel
designated by the RC will meet at

                                       15
<PAGE>

least on a semi-annual basis, unless otherwise agreed in writing, during (i) the
Term and (ii) the pendency of any patent applications claiming Research Program
Inventions, to coordinate, discuss, review and implement patent filing and
prosecution strategy.

     6.3  Failure to Prosecute or Pay.  In the event that a party declines to
          ----------------------------
file or, having filed, fails to further prosecute or maintain any jointly owned
Patent Right, or conduct any interferences, re-examinations, reissues, or
oppositions relating thereto, or pay its share of any of the expenses in
relation to any of the foregoing, then the other party shall have the right to
prepare, file, prosecute and maintain such Patent Right, and conduct any
interferences, re-examinations, reissues or oppositions relating thereto at its
sole expense.  In such event, the funding party shall thereafter be the sole
owner of the subject Patent Right and the non-funding party shall make any
assignment necessary to achieve such ownership position, in accordance with the
provisions of the second sentence of Section 5.4 hereof.

     6.4  Enforcement.  The RC shall determine, from time to time, the party or
          -------------
parties (i) responsible for the enforcement of Patent Rights arising under this
Agreement, and (ii) that shall bear the costs arising under this Section 6.4.

     6.5  Infringement Claims.  If the manufacture, sale or use of any Jointly
          --------------------
Owned Rights or any of the parties' respective technologies results in any
claim, suit or proceeding alleging patent infringement against 3DP or BIOCRYST
(or their respective Affiliates), such party shall promptly notify the other
party hereto in writing setting forth the facts of such claim in reasonable
detail.  The party subject to such claim shall have the exclusive right and
obligation to defend and control the defense of any such claim, suit or
proceeding, at its own expense, using counsel of its own choice; provided,
                                                                ---------
however, such party shall not enter into any settlement which makes any
-------
admission or concession in relation to any Jointly Owned Rights or any of the
parties' respective technologies without the prior written consent of the other
party. The party subject to the claim shall keep the other party hereto
reasonably informed of all material developments in connection with any such
claim, suit or proceeding, and such other party shall cooperate with the party
subject to the claim in connection with such claim. If both parties are subject
to such claim, they shall each cooperate with the other in connection with
defending such claim.

                                   ARTICLE 7

                                CONFIDENTIALITY

     7.1  Confidential Information.  Except as otherwise expressly provided
          ------------------------
herein, the parties agree that a party receiving Confidential Information ("the
Receiving Party") from the other party (the "Disclosing Party") shall not,
except as expressly provided in this Article 7, disclose to any Third Party or
use for any purpose any Confidential Information furnished to it by the
Disclosing Party hereto pursuant to this Agreement, except to the extent that it
can be established by the Receiving Party by written records that such
information:

               (a)  was already known to the Receiving Party, other than under
          an obligation of confidentiality, at the time of disclosure;

                                       16
<PAGE>

               (b)  was generally available to the public or otherwise part of
          the public domain at the time of its disclosure to the Receiving
          Party;

               (c)  became generally available to the public or otherwise part
          of the public domain after its disclosure and other than through any
          act or omission of the Receiving Party in breach of this Agreement;

               (d)  was lawfully disclosed to the Receiving Party, other than
          under an obligation of confidentiality, by a Third Party who had no
          obligation to the Disclosing Party not to disclose such information to
          others;

               (e)  was independently developed by employees of the Receiving
          Party having no knowledge of such Confidential Information; or

               (f)  is required to be disclosed pursuant to applicable law,
          governmental rule or regulation or rule or regulation of any
          securities exchange, provided the Receiving Party uses reasonable
          efforts to limit disclosure and to obtain confidential treatment or a
          protective order and has allowed the Disclosing Party to participate
          in the proceedings

   7.2    Permitted Use and Disclosures.  Each party hereto may use or disclose
          ------------------------------
Confidential Information disclosed to it by the other party only to the extent
such use or disclosure is reasonably necessary and permitted in the exercise of
such rights granted hereunder and the other agreements contemplated hereby,
including without limitation in (i) conducting the Research Program internally
(including conducting the Research Program through Consultants), (ii) filing or
prosecuting patent applications, or prosecuting or defending litigation, (iii)
complying with applicable law, governmental regulation or court order, or (iv)
submitting information to tax or other governmental authorities; provided, that
if a party is required to make any such disclosure of another party's
Confidential Information, such party will give reasonable advance notice to the
other party of such disclosure and, save to the extent inappropriate in the case
of patent applications, will use its reasonable commercial efforts to secure
confidential treatment of such information in consultation with the other party
prior to its disclosure (whether through protective orders or otherwise) and
disclose only the minimum necessary to comply with such requirements.

   7.3    Nondisclosure of Terms.  Each of the parties hereto agrees not to
          -----------------------
disclose the terms of this Agreement to any Third Party (except any
Consultants,) without the prior written consent of the other party hereto, which
consent shall not be unreasonably withheld, except to such party's attorneys,
advisors, investors and others on a need to know basis under circumstances that
reasonably ensure the confidentiality thereof, or to the extent required by
applicable law. In addition, BIOCRYST and 3DP may make public statements
regarding the progress of the Research Program and other matters regarding the
Research Program (i) without the other party's prior consent to the extent
required by applicable law, rules or regulations, and (ii) otherwise following
consultation and mutual agreement with the other party, the consent of neither
party to be unreasonably withheld. In the event that either party is required to
file a copy of this Agreement with the Securities and Exchange Commission or
equivalent entity, such party

                                       17
<PAGE>

shall first provide the other party with an opportunity to review the form of
the copy of this Agreement which such party intends to file.

   7.4    Publication.  Any manuscript by 3DP or BIOCRYST or its Affiliates
          ------------
describing the Research Results or any other scientific results of the Research
Program to be published during the Term of this Agreement or within twelve (12)
months of the effective date of termination or expiration of this Agreement
shall be subject to the prior review of the parties at least ninety (90) days
prior to submission. Further, to avoid loss of Patent Rights as a result of
premature public disclosure of patentable information, the Receiving Party shall
notify the Disclosing Party in writing within thirty (30) days after receipt of
any disclosure whether the Receiving Party desires that the parties file a
patent application on any Research Program Invention disclosed in such Research
Results or other scientific results. In the event that the Receiving Party
desires that the parties file such a patent application, the Disclosing Party
shall withhold publication or disclosure of such Research Results or other
scientific results until the earlier of (i) a patent application is filed
thereon, or (ii) the parties determine after consultation that no patentable
invention exists, or (iii) one (1) year after receipt by the Disclosing Party of
the Receiving Party's written notice of the Receiving Party's desire that the
parties file such patent application, or such other period as is reasonable for
seeking patent protection. Further, if such Research Results or any other
scientific results contain information that is subject to use and nondisclosure
restrictions under this Article 7, the Disclosing Party agrees to remove such
information from the proposed publication or disclosure. Following the filing of
any patent application under this Agreement, in the eighteen (18) month period
prior to the publication of such a patent application neither party shall make
any public disclosure regarding any invention claimed in such patent application
without the prior consent of the other party.

   7.5    Survival.  The parties agree that the confidentiality obligations
          --------
under this Article 7 shall survive any termination or expiration of this
Agreement and shall remain in effect indefinitely.

                                   ARTICLE 8

                        REPRESENTATIONS AND WARRANTIES

   8.1    General.  Each party represents and warrants to the other party that
          -------
as of the Effective Date: (i) it has the legal right and authority to extend the
rights granted in this Agreement; (ii) it has the legal right and authority to
enter into this Agreement and to perform all of its obligations hereunder; (iii)
all consents, approvals and authorizations of all governmental authorities and
other persons required to be obtained by such party in connection with this
Agreement and its responsibilities and activities hereunder have been obtained;
(iv) its execution, delivery and performance of this Agreement does not and will
not conflict with, or constitute a breach or default under, or require the
consent of any Third Party under, its charter documents or any material license,
loan or other agreement, contract, commitment or instrument to which it is a
party or any of its assets are bound or violate any provision of law, statute,
rule or regulation or any ruling, writ, injunction, order, judgment or decree of
any court, administrative agency or other governmental body; (v) when executed
by both parties, this Agreement will constitute the valid and legally binding
obligation of such party and shall be enforceable against such party in
accordance with its terms; (vi) it has not previously granted, and during the
Term of this

                                       18
<PAGE>

Agreement will not make any Commitment of, or grant, any rights which in any way
conflict with the rights granted herein; and (vii) there are no existing or
threatened actions, suits or claims pending or, to the best of its knowledge
threatened against it that may affect the performance of its obligations under
the Agreement.

   8.2    Third Party Obligations.  Each party represents to the other that the
          ------------------------
Third Party Obligations set forth on Exhibit D is a full and complete list of
                                     ---------
such party's Third Party Obligations that are applicable to the Research Program
or development and commercialization of products and processes in the Field, and
that such party is not subject to any other Third Party Obligations that are
relevant to the Research Program.

   8.3    Disclaimer.
          ----------

          8.3.1   NEITHER BIOCRYST NOR 3DP MAKES ANY REPRESENTATION OR WARRANTY
OR GUARANTY THAT THE RESEARCH PROGRAM WILL BE SUCCESSFUL IN WHOLE OR IN PART.
THE FAILURE OF THE PARTIES TO SUCCESSFULLY IDENTIFY LEAD COMPOUNDS, OPTIMIZED
LEAD COMPOUNDS, BIOCRYST COMPOUND DERIVATIVES, DEVELOPMENT CANDIDATES OR
PRODUCTS WILL NOT CONSTITUTE A BREACH OF ANY REPRESENTATION OR WARRANTY OR OTHER
OBLIGATION UNDER THIS AGREEMENT.

          8.3.2   NOTHING IN THIS AGREEMENT SHALL BE CONSTRUED AS A
REPRESENTATION MADE, OR WARRANTY GIVEN, BY EITHER PARTY THAT ANY PATENT WILL
ISSUE BASED UPON ANY PENDING PATENT APPLICATION, OR THAT ANY SUCH PATENT WHICH
ISSUES WILL BE VALID.

          8.3.3   EXCEPT AS OTHERWISE EXPRESSLY SET FORTH IN THIS AGREEMENT, THE
PARTIES MAKE NO REPRESENTATIONS AND EXTEND NO WARRANTIES OR CONDITIONS OF ANY
KIND, EITHER EXPRESS OR IMPLIED, WITH RESPECT TO FOCUSED LIBRARIES, 3DP
LIBRARIES, BIOCRYST COMPOUNDS, BIOCRYST TECHNOLOGY, 3DP COMPOUNDS, 3DP
TECHNOLOGY, BIOCRYST COMPOUND DERIVATIVES, LEAD COMPOUNDS, OPTIMIZED LEAD
COMPOUNDS, DEVELOPMENT CANDIDATES, PRODUCTS, RESEARCH RESULTS, OR INFORMATION
DISCLOSED HEREUNDER, INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR ANY PARTICULAR PURPOSE.

                                   ARTICLE 9

                                INDEMNIFICATION

   9.1    BIOCRYST.  BIOCRYST agrees to indemnify, defend and hold 3DP and its
          --------
Affiliates and their directors, officers, employees and agents (the "3DP
Indemnitees") harmless from and against any losses, costs, claims, damages,
liabilities or expense (including without limitation, fees and disbursements of
counsel incurred by the 3DP Indemnitee in any action or proceeding between
BIOCRYST and the 3DP lndemnitee and the 3DP Indemnitee and any third party or
otherwise) (collectively, "Liabilities") arising out of or in connection with
Third Party claims relating to: (i) BIOCRYST's performance of its
responsibilities and activities under this

                                       19
<PAGE>

Agreement, including without limitation, the Research Program; (ii) any breach
by BIOCRYST of its representations and warranties made in Article 8 of this
Agreement, or (iii) any breach by BIOCRYST in the performance or observation of
any covenant, agreement, obligation or provision in this Agreement to be
performed or observed by BIOCRYST, except, in each case, to the extent such
Liabilities result from the gross negligence or intentional misconduct of 3DP.

   9.2    3DP.  3DP agrees to indemnify, defend and hold BIOCRYST and its
          ---
Affiliates and their directors, officers, employees and agents (the "BIOCRYST
Indemnitees") harmless from and against any losses, costs, claims, damages,
liabilities or expense (including without limitation, fees and disbursements of
counsel incurred by the BIOCRYST Indemnitee in any action or proceeding between
3DP and the BIOCRYST Indemnity and the BIOCRYST Indemnitee and any third party
or otherwise) (collectively, "Liabilities") arising out of or in connection with
Third Party claims relating to: (i) 3DP's performance of its responsibilities
and activities under the Research Program; (ii) any breach by 3DP of its
representations and warranties made in Article 8 of this Agreement, or (iii) any
breach by 3DP in the performance or observation of any covenant, agreement,
obligation or provision in this Agreement to be performed or observed by 3DP,
except, in each case, to the extent such Liabilities result from the gross
negligence or intentional misconduct of BIOCRYST.

   9.3    Procedure. A party (the "Indemnitee") that intends to claim
          ---------
indemnification under this Agreement shall promptly notify the other party (the
"Indemnitor") of any claim, demand, action or other proceeding for which the
Indemnitee intends to claim such indemnification, and the Indemnitor shall have
the right to participate in, and, to the extent the Indemnitor so desires, to
assume sole control of the defense thereof with counsel selected by the
Indemnitor; provided, however, that the Indemnitee shall have the absolute right
            --------  -------
to retain its own counsel, with the fees and expenses to be paid by the
Indemnitee. The indemnity obligations under this Agreement shall not apply to
amounts paid in settlement of any loss, claim, damage, liability or action if
such settlement is effected without the consent of the Indemnitor, which consent
shall not be unreasonably withheld or delayed. The failure to deliver notice to
the Indemnitor within a reasonable time after the commencement of any such
action, if prejudicial to Indemnitor's ability to defend such action, shall
relieve the Indemnitor of any liability to the Indemnitee under this Agreement,
but the omission to deliver such notice to the Indemnitor shall not relieve it
of any liability that it may have to the Indemnitee otherwise than under this
Agreement. The Indemnitee, its employees and agents, shall cooperate fully with
the Indemnitor and its legal representatives in the investigation of any action,
claim or liability covered by an indemnification from the Indemnitor. No
Indemnitor shall, without the prior written consent of the Indemnitee, effect
any settlement of any pending or threatened action, suit or proceeding in
respect of which any Indemnitee is or could have been a party and indemnity
could have been sought hereunder by such Indemnitee, unless such settlement
includes an unconditional release of such Indemnitee from all liability on
claims that are the subject matter of such action, suit or proceeding.

   9.4    Insurance.  3DP and BIOCRYST each shall maintain, through self
          ---------
insurance or otherwise, insurance with respect to its activities contemplated by
the Agreement, in such amount and for such term, as 3DP or BIOCRYST,
respectively, customarily maintains covering its similar activities.

                                       20
<PAGE>

                                  ARTICLE 10

                                  ARBITRATION

   10.1   General. Any Unresolved Dispute shall be finally settled at the
          --------
election of either party by final and binding arbitration, conducted in
accordance with the Commercial Arbitration Rules of the American Arbitration
Association. There shall be three (3) arbitrators for each arbitration of an
Unresolved Dispute, unless the parties otherwise agree to only one arbitrator.
On commencement of an arbitration each party shall promptly select one (1)
arbitrator. Each party's selection of an arbitrator shall be in that party's
sole discretion, and such arbitrator may be from a list provided by the AAA or
may be any other person chosen by such party. A party's choice of arbitrator
shall not be subject to challenge by the other party. Within twenty (20) days of
the appointment of the second arbitrator, the two arbitrators shall appoint the
third arbitrator from a list of arbitrators provided by the AAA, who shall be an
attorney or a former judge unless an arbitrator so qualified is unavailable;
provided, however, that if the two existing arbitrators are unable to agree upon
--------  -------
the third arbitrator within such period, either party may request the AAA to
appoint the third arbitrator. The parties agree to use good faith efforts to
choose arbitrators with appropriate qualifications in relation to the Unresolved
Dispute in question. Such qualifications may include, but are not limited to,
expertise in patent law, medicinal chemistry, and/or pharmaceutical product
development (including clinical development and regulatory affairs). The
arbitration shall be held in New York City, unless the parties agree to conduct
the arbitration in another location, and at least one of the arbitrators shall
be an independent expert in pharmaceutical product development. The arbitrators
shall determine what discovery will be permitted, consistent with the goal of
limiting the cost and time which the parties must expend for discovery; provided
the arbitrators shall permit such discovery as they deem necessary to permit an
equitable resolution of the dispute. The arbitrators will apply the laws of the
State of New York in any arbitration, except in relation to patents or other
forms of Proprietary Rights, including but not limited to determination of
inventorship of inventions, or issues relating to interpretation, enforcement,
validity, or ownership of patents or other intellectual property rights, in
which case the arbitrators shall apply the Federal laws of the United States.

   10.2   Final Award and Costs.  In any arbitration pursuant to this Article
          ---------------------
10, the award of the arbitrators shall be final and binding upon the parties and
judgement upon the award may be entered in and enforced by any court of
competent jurisdiction. The costs of the arbitration, including administrative
and the third arbitrator's fees but excluding the fees of the two arbitrators
selected by the parties, shall be shared equally by the parties. Each party
shall bear its own costs and attorneys' and witness, fees and the fees of the
arbitrator that it has selected. A disputed performance or suspended performance
pending the resolution of the arbitration must be completed within thirty (30)
days following the final decision of the arbitrators or such other reasonable
period as the arbitrators determine in a written opinion. Any arbitration
subject to this Article 10 shall be completed, to the extent reasonably possible
in the light of all the circumstances, within one (1) year from the date of the
original filing of the demand for such arbitration with the AAA.

                                       21
<PAGE>

   10.3   Confidentiality.  All arbitration proceedings under this Article 10
          ---------------
shall be confidential and the arbitrators may issue appropriate protective
orders to safeguard the parties' Confidential Information. Except as required by
law, neither party shall make (or instruct any arbitrator to make) any public
announcement with respect to the proceedings or decisions of any arbitration
without the prior written consent of the other party. The existence of any
Unresolved Dispute, the submission of an Unresolved Dispute to arbitration
pursuant to this Article 10, and any award by the arbitrators, shall be kept in
confidence by the parties and the arbitrators, except as required in connection
with the enforcement of such award or implementation of such decisions, as
mutually agreed by the parties or as required by law.

   10.4   Interim Relief. This Article 10 shall not limit the rights of any
          --------------
party to seek in any court of competent jurisdiction interim relief, and only
such interim relief, as may be needed to maintain the status quo or otherwise
                                                      ------ ---
protect the subject matter of the Unresolved Dispute and the arbitration until
the arbitrators shall have been appointed and shall have had an opportunity to
act.

                                  ARTICLE 11

                             TERM AND TERMINATION

   11.1   Term of the Agreement.  The term of this Agreement shall begin as of
          ---------------------
the Effective Date and shall continue in force for a period of twelve (12)
months, extended annually for an additional twelve (12) months unless otherwise
terminated earlier pursuant to this Article 11.

   11.2   Failure to Agree on Research Plan.  If the parties fail to agree upon
          ---------------------------------
and execute a Research Plan within three (3) months from the Effective Date of
this Agreement, then either party may terminate this Agreement immediately by
giving written notice to the other party to such effect.

   11.3   Right to Terminate.  Either party has the right to terminate the
          ------------------
Agreement, with or without cause, upon providing sixty (60) days prior written
notice to the other party.

   11.4   Effect of Termination.
          ---------------------

          11.4.1    Accrued Rights and Obligations. Termination of this
                    ------------------------------
Agreement for any reason shall not release either party hereto from any
liability which, at the time of such termination, has already accrued to the
other party or which is attributable to a period prior to such termination, nor
preclude either party from pursuing any rights, indemnities and remedies it may
have hereunder or at law or in equity with respect to any breach of this
Agreement.

          11.4.2    Return of Materials. Upon any termination of this Agreement,
3DP and BIOCRYST shall promptly return to the other all Confidential Information
received from the other party (except one copy of which may be retained solely
for legal archival purposes, such copy to remain subject to the provisions of
Article 7 hereof).

                                       22
<PAGE>

          11.4.3    Survival. Articles 5, 6, 7, 8, 9, 10 and 2.11 and Sections
2.9, 2. 10 and 2.11 of this Agreement and any accrued rights of payment or
causes of action shall survive the expiration or termination of this Agreement
for any reason.

                                  ARTICLE 12

                                 MISCELLANEOUS

   12.1   Governing Laws.  Except as otherwise specified herein, this Agreement
          --------------
and any dispute arising from the performance or breach hereof shall be governed
by and construed and enforced in accordance with the laws of the state of New
York, without reference to conflict of laws principles thereof.

   12.2   No Implied Licenses.  Only the licenses granted pursuant to the
          -------------------
express terms of this Agreement shall be of any legal force or effect.  No other
license rights shall be created by implication, estoppel or otherwise.

   12.3   Waiver. It is agreed that no waiver by either party hereto of any
          ------
breach or default of any of the covenants or agreements herein set forth shall
be deemed a waiver as to any subsequent and/or similar breach or default.

   12.4   Assignment. This Agreement shall not be assignable by either party to
          ----------
any Third Party without the written consent of the other party hereto, except
either party may assign this Agreement, without such consent, to either (i) one
of its Affiliates, or (ii) an entity that acquires all or substantially all of
the business, assets or stock of such party to which this Agreement pertains,
whether by merger, reorganization, acquisition, sale, or otherwise, provided, in
each case, that the assignor remains liable for all of its obligations hereunder
and for performance by the assignee. This Agreement shall be binding upon and
accrue to the benefit of any permitted assignee, and any such assignee shall
agree to perform the obligations of the assignor.

   12.5   Independent Contractors. The parties expressly agree that the
          -----------------------
relationship between them is that of independent contractors. The parties hereto
shall not be deemed to be agents, partners or joint venturers of the other for
any purpose as a result of this Agreement or the transactions contemplated
hereby.

   12.6   Compliance. In connection with their respective activities under this
          ----------
Agreement, the parties and their Affiliates shall fully comply in all material
respects with the requirements of any and all applicable laws, regulations,
rules and orders of any governmental body having jurisdiction over the exercise
of right under this Agreement including, without limitations those applicable to
the research, discovery, development, patent prosecution, manufacture,
distribution, import and export and sale of any products pursuant to this
Agreement.

   12.7   Export Control. The parties agree not to remove or export from the
          --------------
United States or re-export from anywhere any part of the Lead Compounds,
BIOCRYST Compound Derivatives, Optimized Lead Compounds, Research Results,
Development Candidates, or any direct product thereof to Afghanistan, the
Peoples' Republic of China or any Group Q, S, W, Y

                                       23
<PAGE>

or Z country (as specified in Supplement No. I to Section 770 of the U.S. Export
Administration Regulations, or a successor thereto) or otherwise except in
compliance with and with all licenses and approvals required under applicable
export laws and regulations, including without limitation, those of the U.S.
Department of Commerce.

   12.8   Notices. All notices, reports, consents, requests and other
          --------
communications hereunder shall be in writing and shall be personally delivered,
sent by registered or certified mail, postage prepaid, or by facsimile (with
proof of receipt and a confirmation copy sent by registered or certified mail,
postage prepaid) or sent by overnight delivery service, in each case to the
respective address specified below, or such other address as may be specified in
writing to the other party hereto and shall be deemed to have been given upon
receipt:

If to 3DP:                    3-Dimensional Pharmaceuticals, Inc.
                              665 Stockton Drive, Suite 104
                              Exton, PA 19341
                              U.S.A.
                              Attn:  Chief Executive Officer
                              Fax No.:  (610) 458-8258

with a copy to:               Morgan Lewis & Bockius LLP
                              2000 One Logan Square
                              Philadelphia, PA 19103
                              Attn:  David R. King, Esq.
                              Fax No.:  (215) 963-5299

BIOCRYST:                     BioCryst Pharmaceuticals, Inc.
                              2190 Parkway Lake Drive
                              Birmingham, AL  35244
                              Attn: President
                              Fax No.:  (205) 444-4640

With a copy to:               Brobeck, Phleger & Harrison LLP
                              1301 Avenue of the Americas,
                              ---------------------------
                              New York, New York 10019
                              Attn:  Richard R. Plumridge, Esq.
                              Fax No.: (212) 586-7878

   12.9   Severability.  In the event that any provision of this Agreement
          -------------
becomes or is declared by a court of competent jurisdiction to be illegal,
unenforceable or void, this Agreement shall continue in full force and effect
without said provision, and the parties shall amend this

                                       24
<PAGE>

Agreement to the extent feasible to lawfully include the substance of the
excluded term to as fully as possible realize the intent of the parties and
their commercial bargain.

   12.10  SPECIAL, INCIDENTAL AND CONSEOUENTIAL DAMAGES. NEITHER PARTY WILL BE
          ----------------------------------------------
LIABLE UNDER ANY CONTRACT, NEGLIGENCE, STRICT LIABILITY OR OTHER THEORY FOR ANY
SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES WITH RESPECT TO ANY SUBJECT MATTER
OF THIS AGREEMENT EXCEPT FOR A BREACH OF ARTICLE 7.

   12.11  Force Majeure.  Neither party shall lose any rights hereunder or be
          --------------
liable to the other party for damages or losses or be deemed to have defaulted
under or breached this Agreement on account of failure of performance by the
defaulting party if the failure is occasioned by war, acts of war (whether
declared or not), strike, insurrections, riots, civil commotions, fire, act of
god, earthquake, flood, lockout or other labor disturbances, embargo,
governmental acts or orders or restrictions, failure of suppliers, or any other
reason where failure to perform is beyond the reasonable control and not caused
by the negligence, intentional conduct or misconduct of the non-performing party
and such party has exerted all commercially reasonable efforts to avoid and
remedy such force majeure; provided, however, that in no event shall a party be
                           --------  -------
required to settle any labor dispute or disturbance.

   12.12  Entire Agreement.  This Agreement and the Exhibits attached hereto
          -----------------
constitute the entire agreement, both written and oral, between the parties with
respect to the subject matter hereof, and all prior agreements respecting the
subject matter hereof, either written or oral, expressed or implied, shall be
abrogated, canceled, and are null and void and of no effect. No amendment or
change hereof or addition hereto shall be effective or binding on either of the
parties hereto unless reduced to writing and executed by the respective duly
authorized representatives of the parties.

   12.13  Headings.  The captions to the several Articles and Sections hereof
          --------
are not a part of this Agreement, but are included merely for convenience of
reference and location only and shall not affect its meaning or interpretation.

   12.14  Counterparts.  This Agreement may be executed in two or more
          ------------
counterparts, each of which shall be deemed to be an original and all of which
together shall be deemed to be one and the same instrument.

                                       25
<PAGE>

     IN WITNESS WHEREOF, the parties hereto have caused this Research
Collaboration Agreement to be duly executed by their authorized representatives
and delivered in duplicate originals as of the Effective Date.

3-DIMENSIONAL                         BIOCRYST
PHARMACEUTICALS, INC.                 PHARMACEUTICALS, INC.

By:/s/ Thomas P. Stagnaro             By:/s/ Charles E. Bugg
   --------------------------------      ------------------------------------
Name:        Thomas P. Stagnaro       Name:    Charles E. Bugg
     ------------------------------        ----------------------------------
Title: President and CEO              Title: Chairman, President and CEO
       ----------------------------          --------------------------------

                                       26
<PAGE>

                                                                  DRAFT 10/17/96
                                   EXHIBIT A

                                     [**]

**This entire page of this Exhibit and the next four pages of this Exhibit have
been omitted based upon a request for confidential treatment that has been filed
with the Commission. The omitted pages have been filed separately with the
Commission.

                                      A-1

<PAGE>

                                   EXHIBIT B

                                      [**]

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission. The omitted
portions have been filed separately with the Commission.

                                      B-1
<PAGE>

                                   EXHIBIT C
               Initial Representatives on the Research Committee
               -------------------------------------------------

1.   Initial Representatives of 3DP:
     ------------------------------

     [**]

2.   Initial Representatives of BIOCRYST
     -----------------------------------

     [**]

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission. The omitted
portions have been filed separately with the Commission.

                                      C-1
<PAGE>

                                   EXHIBIT D

                            Third Party Obligations
                            -----------------------

                                      [**]

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission. The omitted
portions have been filed separately with the Commission.

                                      D-1
<PAGE>

                                   [Exhibit]

                                      [**]

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission. The omitted
portions have been filed separately with the Commission.
<PAGE>

              Amendment No. 1 to Research Collaboration Agreement
              ---------------------------------------------------

     THIS IS AMENDMENT NO. 1 TO RESEARCH COLLABORATION AGREEMENT effective as of
October 18,1996 between 3-Dimensional Pharmaceuticals, Inc., a Delaware
corporation ("3DP"), and BIOCRYST Pharmaceuticals, Inc., a Delaware corporation
("BioCryst").

                                   Background
                                   ----------

     WHEREAS, 3DP and BioCryst are parties to a Research Collaboration Agreement
dated October 18, 1996 (the "Agreement"), and WHEREAS, the parties desire to
amend the Agreement as set forth below.

     NOW, THEREFORE, for and in consideration of the foregoing premises and the
mutual promises and covenants contained herein, the parties agree as follows:

                                     Terms
                                     -----

1.   Amendment of Agreement
     ----------------------

     1.1     The Agreement is hereby amended by adding Sections 1.6a, 1.10a,
2.2.1(i), 2.2.2(g), 3.6, 4.4 and 4.5 to read in full as follows:

             1.6a  "BIOCRYST Library" shall mean any chemical compound library
                    ----------------
             developed by or on behalf of BIOCRYST independently of the Research
             Program for activity outside the Field using BIOCRYST Technology
             and excluding Focused Libraries.

             1.10a "Counter Screening Targets" shall mean those enzymes and
                    -------------------------
             proteins set forth in Exhibit E, as amended from time to time in
             accordance with Section 4.5.

             2.2.1

                    (i)   at the sole discretion of BIOCRYST, selecting and
                    screening compounds contained in BIOCRYST Libraries to
                    discover Lead Compounds or to develop structure-activity
                    relationships.

             2.2.2

                    (g)   at the sole discretion of 3DP, selecting and screening
                    3DP Compounds to discover Lead Compounds or to develop
                    structure-activity relationships.

                                       1
<PAGE>

               3.6  Materials Transfer Agreement. Any 3DP Compounds which do
                    ----------------------------
               not meet the criteria for Lead Compounds, but which are
               identified by the Research Committee for further study to develop
               structure-activity relationships may, with 3DP's consent, be
               transferred to BIOCRYST for further study. Such transferred 3DP
               Compounds will be transferred and tested pursuant to the
               Materials Transfer Agreement in the form of Exhibit F hereto and
               executed by the parties herewith. Compounds contained in BioCryst
               Libraries which do not meet the criteria for Lead Compounds, but
               which are identified by the Research Committee for screening or
               for further study to develop structure-activity relationships
               may, with BioCryst's consent, be transferred from BIOCRYST to 3DP
               for further study. Such transferred compounds will be transferred
               and tested pursuant to the Materials Transfer Agreement in the
               form of Exhibit G hereto and executed by the parties herewith.

               4.4  Both parties agree that their respective research outside of
               the Field may identify compounds which also have activity within
               the Field and that such research does not violate the exclusivity
               commitment set forth in section 4.1 or 4.2.

               4.5  Either party may amend Exhibit E to add a new Counter
               Screening Target by written notice to the other, provided that
               such amendment shall have no effect on any rights under this
               Agreement which arose prior to such amendment, including without
               limitation any rights relating to any Research Results, Lead
               Compounds, Optimized Lead Compounds, BIOCRYST Compound
               Derivatives or Research Program Inventions that were conceived,
               identified, isolated, created or first reduced to practice prior
               to the date of such notice.

     1.2  The Agreement is hereby amended  by  adding  Exhibits  E,  F,  and  G
thereto  in  the form attached hereto.

     1.3  The Agreement is hereby amended by amending and restating Sections
1.9, 1.12, 2.4 and 5.1 to read in full as follows:

               1.9  "Confidential Information" means all non-public, proprietary
                     ------------------------
               or otherwise confidential information, now owned, licensed or
               controlled or hereafter acquired, developed, owned, licensed or
               controlled by a disclosing party or any of its Affiliates during
               the Term of this Agreement and which is disclosed in writing or
               (if disclosed orally) confirmed in writing and marked
               "confidential". Confidential Information shall include, but not
               be limited to: (i) BIOCRYST Libraries, BIOCRYST Compounds and
               BIOCRYST Technology; (ii) the 3DP Libraries, the 3DP Compounds
               and the 3DP Technology; (iii) Focused Libraries and Research
               Results; (iv) Lead Compounds, BIOCRYST Compound Derivatives,
               Optimized Lead Compounds, and Development Candidates; and (v)
               Products prior to their first commercial sale.

                                       2
<PAGE>

               1.12  "Field" Shall mean inhibitors of the Complement System
                      -----
               enzymes and proteins specified in Exhibit B, as amended and
               attached hereto, which inhibitors have [**] (or other applicable
               assays as agreed to by the Research Committee), provided that
               such inhibitors (i) with respect to the [**] (now or as hereafter
               amended) have [**] (or other applicable assays as agreed to by
               the Research Committee).

               2.4   BIOCRYST Compounds, BIOCRYST Libraries and BIOCRYST
                     ---------------------------------------------------
               Technology. 3DP acknowledges that BIOCRYST (i) has previously
               ----------
               expended substantial financial and research resources in relation
               to its work in the Field, the BIOCRYST Libraries and the BIOCRYST
               Technology that exists as of the Effective Date, (ii) has
               identified the BIOCRYST Compounds and (iii) has an on-going
               research, development and commercialization program in relation
               to the BIOCRYST Compounds in the FIELD which BIOCRYST shall be
               conducting independently of the arrangements under this
               Agreement.  Notwithstanding any other provisions of this
               Agreement to the contrary, the parties agree that BIOCRYST shall
               be free to (a) conduct its independent research, development and
               commercialization program in the FIELD in relation to BIOCRYST
               Compounds using BIOCRYST Technology, (b) research, develop and
               commercialize BIOCRYST Compounds and any product or service based
               thereon in the Field, without restriction, reference or payment
               to 3DP, (c) conduct any independent research, development and
               commercialization program outside the Field in relation to
               BIOCRYST Compounds, the BIOCRYST Libraries and BIOCRYST
               Technology and (d)  research, develop and commercialize BIOCRYST
               Compounds, the BIOCRYST Libraries and BIOCRYST Technology and any
               product or service based thereon outside the FIELD, without
               restriction, reference or payment to 3DP.

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission. The omitted
portions have been filed separately with the Commission.

                                       3
<PAGE>

               5.1  Retained Rights.  The parties agree that they shall each
                    ---------------
               separately retain all their respective rights, title and interest
               in relation to any Invention, technology, know-how, compound,
               product, process, information or Proprietary Right which they
               either (i) held prior to the Effective Date or (ii) they
               conceive, identify, isolate, create, first reduce to practice,
               license or acquire entirely independently of the Research Program
               (which shall be subject to reasonable documented verification).
               Nothing contained herein shall be deemed to create a license or
               right under any of the foregoing for purposes outside the scope
               of the Research Program, including without limitation, the
               development and commercialization of Development Candidates.  The
               parties specifically agree that, subject to the licenses granted
               herein, (i) BIOCRYST shall retain all right, title and interest
               (including, but not limited to any Proprietary Rights) that
               BIOCRYST holds in relation to BIOCRYST Compounds, BIOCRYST
               Libraries and BIOCRYST Technology and (ii) 3DP shall retain all
               right, title and interest (including, but not limited to, any
               Proprietary Rights) that 3DP holds in relation to the 3DP
               Compounds, 3DP Libraries and 3DP Technology. 3DP shall retain
               full right, title and interest in any 3DP Compounds that have
               activity outside the Field which have been tested within the
               Field solely to establish the potential of side-effects.
               BIOCRYST shall retain full right, title and interest in any
               BioCryst Compounds having activity outside the Field which have
               been tested within the Field solely to establish the potential
               for side-effects.

     1.4  The Agreement is hereby amended by amending and restating Exhibit B in
the form attached hereto.

2.   Miscellaneous.
     -------------

     2.1  Governing Law; Parties in Interest.  This Amendment shall be governed
          ----------------------------------
by the laws of the State of Delaware, without regard to the conflicts of laws
thereof, and shall bind and inure to the benefit of the parties hereby and their
respective successors and assigns.

     2.2  Counterparts.  This Amendment may be executed simultaneously in two or
          ------------
more counterparts, each of which shall be deemed an original, but all of which
together shall constitute one and the same instrument.

     2.3  Full Force and Effect.  Except as expressly set forth herein, the
          ---------------------
Agreement remains unchanged and in full force and effect.

                                       4
<PAGE>

IN WITNESS WHEREOF, the parties have executed and delivered this Agreement on
the date written below.

                              3-DIMENSIONAL PHARMACEUTICALS, INC.

                              By:    /s/ F. Raymond Salemme
                                 --------------------------------

                              Dated: June 18, 1999
                                    -----------------------------

                              BIOCRYST PHARMACEUTICALS, INC.

                              By:    /s/ Charles E. Bugg
                                   ------------------------------

                              Dated: June 18, 1999
                                    -----------------------------

                                       5
<PAGE>

                                   EXHIBIT B

                                     [**]

**This page and the next page of this Exhibit have been omitted based upon a
request for confidential treatment that has been filed with the Commission.
The omitted pages have been filed separately with the Commission.

                                      B-1
<PAGE>

                                   EXHIBIT E

                                     [**]

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission. The omitted
portions have been filed separately with the Commission.

                                      E-1
<PAGE>

                                   EXHIBIT F

                         MATERIALS TRANSFER AGREEMENT
                         ----------------------------

     This MATERIALS TRANSFER AGREEMENT ("MTA"), is made by and between
3DIMENSIONAL PHARMACEUTICALS, INC. ("3DP"), a corporation having its principal
place of business at Eagleview Corporate Center, 665 Stockton Drive, Suite 104,
Exton, Pennsylvania 19341, and BIOCRYST PHARMACEUFICALS, INC. (THE RECIPIENT), A
Delaware corporation having a principal place of business at 2190 Parkway Lake
Drive, Birmingham, Alabama 35244.

                                   RECITALS
                                   --------

     WHEREAS, 3DP and RECIPIENT are parties to the Research Collaboration
Agreement dated October 18, 1996, as amended ("the Agreement").  WHEREAS the
parties desire to set forth herein the terms and conditions under which 3DP may
transfer to RECIPIENT certain 3DP compounds pursuant to Section 3.6 of the
Agreement.  Capitalized terms used herein without definition have the meaning
set forth in the Agreement.

                                   AGREEMENT
                                   ---------

     1.00 Definitions. As used in this Materials Transfer Agreement, the
          -----------
following terms shall have the following meanings:

     1.01 "Effective Date" means the date hereof.

     1.02 "Compound" means any 3DP Compound transferred to RECIPIENT by 3DP
          after June 1, 1999 pursuant to Section 3.6 of the Agreement and
          identified as such by 3DP in writing.

     1.03 "Experimental Tests" shall mean any test performed an a Compound by
          RECIPIENT. Such tests consist only of:

          a.   [**]

          b.   [**]

          c.   Other assays or experiments identified by the Research Committee.

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission. The omitted
portions have been filed separately With the Commission.

                                      F-1
<PAGE>

Experimental tests performed by RECIPIENT shall be limited to those listed above
in this Section 1.03. Under no circumstances shall RECIPIENT conduct any other
Experimental Tests an a Compound, including, but not limited to, tests related
to determining the chemical composition of such Compound.

     1.04 "Technology" means all technical information, developments, data,
results, formulae and processes relating to any Compound that result from
RECIPIENT's tests of such Compound.

     2.00 Transfer of Material.  RECIPIENT agrees to protect the confidentiality
          --------------------
of any Compound and any Technology resulting from the testing of such Compound
as provided in Article 4.00.

     2.01 RECIPIENT agrees to return any and all of the remaining sample of any
Compounds upon termination of the Agreement.

     3.00 Data and Documents
          ------------------

     3.01 Access to Compound.  Access to the Compound will be limited and
controlled.  RECIPIENT shall provide to 3DP upon written request a list of the
names of all access to any such Compound and the dates of such access.

     3.02 Access to Documents Relating to Compound. Access to documents relating
to any Compound will be limited and controlled. Such documents will be clearly
marked m the face thereof with an appropriate indication of their confidential
status. As noted below in Paragraph 4.00, RECIPIENT may retain one copy of all
documents relating to such for archive purposes. The obligations specified in
this paragraph continue with respect to the archive copy of the documents
retained by RECIPIENT.

     3.03 Testing Relating to Compound.  RECIPIENT shall provide to 3DP a
summary of each experiment or test performed on any Compound, the person
performing such experiment or test, the date of such experiment or test, and the
quantities of such Compound used in the experiment or test. 3DP shall keep this
information confidential as provided in Article 4.00.

     3.04 Return of Compound and Documents Relating to Compound.  When this MTA
is terminated, RECIPIENT agrees to return all unused samples of Compound and all
documents relating to such Compound, including all copies of such documents, to
3DP, provided, however, that RECIPIENT may retain one copy of all documents
relating to such Compounds for archive purposes.  RECIPIENT agrees to continue
to maintain the confidentiality of the documents relating to any such Compounds
as provided by Article 4.00.

                                      F-2
<PAGE>

     4.00 Confidentiality and Ownership of Proprietary Information.
          --------------------------------------------------------
Notwithstanding anything to the contrary set forth herein, 3DP and RECIPIENT
agree to maintain the confidentiality of all of the other party's Confidential
Information, provided or generated in connection with this MTA and each party
will promptly return to the other party all copies of written materials, whether
secret or otherwise, which have been so provided or generated except for one
archive copy. 3DP and RECIPIENT further agree that they will not use such
information or disclose it to third parties, except within the scope of this
MTA.  Upon termination of this MTA, this obligation will continue for a period
of five (5) years from the date of termination.  For the purposes of this MTA,
Confidential Information shall mean all nonpublic, proprietary or otherwise
confidential information, now owned, licensed or controlled or hereafter
acquired, developed, owned, licensed or controlled by a disclosing party during
the term of this MTA and which is disclosed in writing or (if disclosed orally)
confirmed in writing and marked "Confidential".  Confidential Information may
include, but is not limited to: (i) chemical compounds; (ii) Technology; and
(iii) the existence and details of this MTA.  Ownership of all Technology and
related intellectual property rights created under this MTA shall be governed
the Terms of the Agreement.  Information will not be considered Confidential
Information hereunder that:

          a.   is publicly known when disclosed by the disclosing party;
          b.   later becomes publicly known without fault of the receiving
               party;
          c.   is known by the receiving party before disclosure by the
               disclosing party
          d.   is independently discovered by the receiving party without use of
               the confidential information; or
          e.   is required to be disclosed by court order or regulation.

     5.00 Warranty
          --------

     5.01 3DP warrants to RECIPIENT that it has the lawful right to transfer
samples of Compound.

     5.02 Nothing in this MTA:

          a.   is a warranty or representation that anything made, used, sold,
               or offered for sale under any license from 3DP is or will be free
               from infringement of patents of third parties;

          b.   is an obligation to bring or prosecute actions or  suits  against
               third  parties for patent infringement.

     6.00 Term and Termination of MTA
          ---------------------------

     6.01 The term of this MTA shall commence on the Effective Date.

     6.02 This MTA will terminate upon termination of the Agreement, provided
that the provisions of Section 3.04 and 4.00 will survive such termination.

                                      F-3
<PAGE>

     7.00 Miscellaneous
          -------------

     7.01 Notices
          -------

          (a)  All notices to, demands, consents, or communications which any
     party may desire or may be required to give to the other must be in
     writing, shall be effective upon receipt in the United States after having
     been sent by registered or certified mail or sent by facsimile
     transmission.  Receipt shall be presumed on the date of proper transmission
     as to facsimile transmissions and otherwise within three (3) days as to
     notices given within the United States.

          (b)  Any notice required or permitted by this MTA shall be addressed
     to the Party in question as follows:

               If to 3DP:          3-Dimensional Pharmaceuticals, Inc.
                                   Eagleview Corporate Center
                                   665 Stockton Drive, Suite 104
                                   Exton, PA 19341
                                   Attention: Chief Executive Officer

               If to RECIPIENT:    BioCryst Pharmaceuticals Inc.
                                   2190 Parkway Lake Drive
                                   Birmingham, AL 35244
                                   Attention: Chief Executive Officer

or to such other address or addresses as may from time to time be given in
writing by either party to the other pursuant to the terms hereof.

7.02 Sole Agreement.  This MTA constitutes and embodies the entire Agreement
     --------------
between the  Parties with respect to the subject matter hereof, and supersedes
all previous agreements, understandings, negotiations, discussions, offers and
acceptances with respect to such matter.  This MTA may not be modified except in
writing signed by authorized representatives of both parties and may not be
assigned by either party without the written consent of the other, which consent
shall not be unreasonably withheld or delayed.

7.03 Severability.  Any of the provisions of this MTA which are determined to be
     ------------
invalid or unenforceable in any jurisdiction shall be ineffective to the extent
of such invalidity or unenforceability in such jurisdiction, without rendering
invalid or unenforceable the remaining provisions hereof or affecting the
validity or unenforceability of any of the terms of the MTA in any other
jurisdiction.

7.04 No Third Party Benefits.  Nothing in this MTA, express or implied, is
     -----------------------
intended to confer on any person other than the parties hereto or their
permitted assigns, any benefits, rights or remedies.

7.05 Governing Law.  This MTA shall be governed by Delaware law.
     -------------

                                      F-4
<PAGE>

7.06 No Waiver.  A waiver by either party of a breach or violation of any
     ---------
provision of this MTA will not constitute or be construed as a waiver of any
subsequent breach or violation of that provision or as a waiver of any breach or
violation of any other provision of this MTA.

7.07 Headings.  Any headings and captions included herein are for convenience of
     --------
reference only and shall not be used to construe this MTA.

7.08 Consequential Damages.  Neither party shall be liable for any or damage
     ---------------------
arising out of or resulting from anything made available hereunder, or for the
exercise by the other party of any rights granted hereunder, nor be liable to
the other party for consequential damages under any circumstances.

7.09 Agency.  This MTA does not constitute either party hereto the agent of the
     ------
other party for any purpose whatsoever, nor does either party thereto have the
right or authority to assume, create, or incur any liability of any kind,
express, or implied, against or in the name or on behalf of the other party.

IN WITNESS WHEREOF, the parties have executed and delivered this Agreement as of
the date written below.

                                             3-DIMENSIONAL PHARMACEUTICALS, INC.

                                             By:   /s/ F. Raymond Salemme
                                                 -------------------------------

                                             Dated: June 18, 1999
                                                   -----------------------------

                                             BIOCRYST PHARMACEUTICALS, INC.

                                             By:   /s/ Charles E. Bugg
                                                 -------------------------------

                                             Dated: June 18, 1999
                                                   -----------------------------

                                      F-5
<PAGE>

                                   EXHIBIT G
                         MATERIALS TRANSFER AGREEMENT
                         ----------------------------

     This MATERIALS TRANSFER AGREEMENT ("MTA"), is made by and between, BIOCRYST
PHARMACELMCALS, INC. ("BIOCRYST"), a Delaware corporation having a principal
place of business at 2190 Parkway Lake Drive, Birmingham, Alabama 35244, and 3-
DIMENSIONAL PHARMACEUTICALS, INC. (THE RECIPIENT), a corporation having its
principal place of business at Eagleview Corporate Center, 665 Stockton Drive,
Suite 104, Exton, Pennsylvania 19341.

                                   RECITALS
                                   --------

     WHEREAS, BioCryst and RECIPIENT are parties to the Research Collaboration
Agreement dated October 18, 1996, as amended ("the Agreement"). WHEREAS the
parties desire to set forth herein the terms and conditions under which BioCryst
may transfer to RECIPIENT certain compounds pursuant to Section 3.6 of the
Agreement.  Capitalized terms used herein without definition have the meaning
set forth in the Agreement.

                                   AGREEMENT
                                   ---------

     1.00 Definitions.  As used in this Materials Transfer Agreement, the
          -----------
following terms shall have the following meanings:

     1.01 "Effective Date" means the date hereof.

     1.02 "Compound" means any compound transferred to RECIPIENT by BioCryst
after June 1, 1999 pursuant to Section 3.6 of the Agreement and identified as
such by BioCryst in writing.

     1.03 "Experimental Tests" shall mean any test performed an a Compound by
RECIPIENT.  Such tests consist only of:

          a.   [**]
          b.   [**]
          c.   Other assays or experiments identified by the Research Committee.

Experimental tests performed by RECIPIENT shall be limited to those listed above
in this Section 1.03. Under no circumstances shall RECIPIENT conduct any other
Experimental Tests on a Compound, including, but not limited to, tests related
to determining the chemical composition of such Compound.

     1.04 "Technology" means all technical information, developments, data,
results, formulae and processes relating to any Compound that result from
RECIPIENT's tests of such Compound.

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission. The omitted
portions have been filed separately With the Commission.

                                      G-1
<PAGE>

     2.00 Transfer of Material.  RECIPIENT agrees to protect the confidentiality
          --------------------
of any Compound and any Technology resulting from the testing of such Compound
as provided in Article 4.00.

     2.01 RECIPIENT agrees to return any and all of the remaining sample of any
Compounds upon termination of the Agreement.

     3.00 Data and Documents
          ------------------

     3.01 Access to Compound.  Access to Compound will be limited and
controlled.  RECIPIENT shall provide to BIOCRYST upon written request a list of
the names of all persons having access to any such Compound and the dates of
such access.

     3.02 Access to Documents Relating to Compound.  Access to documents
relating to any Compound will be limited and controlled.  Such documents will be
clearly marked on the face thereof with an appropriate indication of their
confidential status.  As noted below in Paragraph 4.00, RECIPIENT may retain one
copy of all documents relating to such Compound for archive purposes.  The
obligations specified in this paragraph continue with respect to the archive
copy of the documents retained by RECIPIENT.

     3.03 Testing Relating to Compound.  RECIPIENT shall provide to BIOCRYST a
summary of each experiment or test performed on any Compound, the person
performing such experiment or test, the date of such experiment or test, and the
quantities of such Compound used in the experiment or test.  BIOCRYST shall keep
this information confidential as provided in Article 4.00.

     3.04 Return of Compound and Documents Relating to Compound.  When this MTA
is terminated, RECIPIENT agrees to return all unused samples of Compound and all
documents relating to such Compound, including all copies of such documents, to
BIOCRYST, provided, however, that RECIPIENT may retain one copy of all documents
relating to such Compounds for archive purposes. RECIPIENT agrees to continue to
maintain the confidentiality of the documents relating to such Compounds as
provided by Article 4.00.

                                      G-2
<PAGE>

     4.00 Confidentiality and Ownership of Proprietary Information.
          --------------------------------------------------------
Notwithstanding anything to the contrary set forth herein, BIOCRYST and
RECIPIENT agree to maintain the confidentiality of all of the other party's
Confidential Information, provided or generated in connection with this MTA and
each party will promptly return to the other party all copies of written
materials, whether secret or otherwise, which have been so provided or generated
except for one archive copy.  BIOCRYST and RECIPIENT further agree that they
will not use such information or disclose it to third parties, except within the
scope of this MTA.  Upon termination of this MTA, this obligation will continue
for a period of five (5) years from the date of termination.  For the purposes
of this MTA, Confidential Information shall mean all nonpublic, proprietary or
otherwise confidential information, now owned, licensed or controlled or
hereafter acquired, developed, owned, licensed or controlled by a disclosing
party during the term of this MTA and which is disclosed in writing or (if
disclosed orally) confirmed in writing and marked "Confidential".  Confidential
Information may include, but is not limited to: (i) chemical compounds; (ii)
Technology; and (iii) the existence and details of this MTA.  Ownership of all
Technology and related intellectual property rights created under this MFA shall
be governed by the Terms of the Agreement.  Information will not be considered
Confidential Information hereunder that:

          a.   is publicly known when disclosed by the disclosing party;
          b.   later becomes publicly known without fault of the receiving
               party;
          c.   is known by the receiving party before disclosure by the
               disclosing party
          d.   is independently discovered by the receiving party without use of
               the confidential information; or
          e.   is required to be disclosed by court order or regulation.

     5.00 Warranty
          --------

     5.01 BIOCRYST warrants to RECIPIENT that it has the lawful right to
transfer samples of Compound.

     5.02 Nothing in this MTA:

          a.   is a warranty or representation that anything made, used, sold,
               or offered for sale under any license from BIOCRYST is or win be
               free from infringement of patents of third parties;

          b.   is an obligation to bring or prosecute actions or suits against
               third parties for patent infringement.

     6.00 Term and Termination of MTA
          ---------------------------

     6.01 The term of this MTA shall commence on the Effective Date.

     6.02 This MTA will terminate upon termination of the Agreement, provided
that the provisions of Section 3.04 and 4.00 will survive such termination.

     7.00 Miscellaneous
          -------------

                                      G-3
<PAGE>

     7.01 Notices
          -------

          (a)  All notices to, demands, consents, or communications which any
party may desire or may be required to give to the other must be in writing,
shall be effective upon receipt in the United States after having been sent by
registered or certified mail or sent by facsimile transmission.  Receipt shall
be presumed on the date of proper transmission as to facsimile transmissions and
otherwise within three (3) days as to notices given within the United States.

          (b)  Any notice required or permitted by this MTA shall be addressed
to the Party in question as follows:

               If to BIOCRYST:    BioCryst Pharmaceuticals Inc.
                                  2190 Parkway Lake Drive
                                  Birmingham, AL 35244
                                  Attention: Chief Executive Officer

               If to RECIPIENT:   3-Dimensional Pharmaceuticals, Inc.
                                  Eagleview Corporate Center
                                  665 Stockton Drive, Suite 104
                                  Exton, PA 19341
                                  Attention: Chief Executive Officer:

or to such other address or addresses as may from time to time be given in
writing by either party to the other pursuant to the terms hereof.

          7.02 Sole Agreement.  This MTA constitutes and embodies the entire
               --------------
Agreement between the Parties with respect to the subject matter hereof, and
supersedes all previous agreements, understandings, negotiations, discussions,
offers and acceptances with respect to such subject matter.  This MTA may not be
modified except in writing signed by authorized representatives of both parties
and may not be assigned by either party without the written consent of the
other, which consent shall not be unreasonably withheld or delayed.

          7.03 Severability.  Any of the provisions of this MTA which are
               ------------
determined to be invalid or unenforceable in any jurisdiction shall be
ineffective to the extent of such invalidity or unenforceability in such
jurisdiction, without rendering invalid or unenforceable the remaining
provisions hereof or affecting the validity or unenforceability of any of the
terms of the MTA in any other jurisdiction.

          7.04 No Third Party Benefits.  Nothing in this MTA, express or
               -----------------------
implied, is intended to confer on any person other than the parties hereto or
their permitted assigns, any benefits, rights or remedies.

          7.05 Governing Law. This MTA shall be governed by Delaware law.
               -------------

          7.06 No Waiver.  A waiver by either party of a breach or violation of
               ---------
any provision of this MTA will not constitute or be construed as a waiver of any
subsequent breach

                                      G-4
<PAGE>

or violation of that provision or as a waiver of any breach or
violation of any other provision of this MTA.

          7.07 Headings.  Any headings and captions included herein are for
               --------
convenience of reference only and shall not be used to construe this MTA.

          7.08 Consequential Damages.  Neither party shall be liable for any
               ---------------------
consequence or damage arising out of or resulting from anything made available
hereunder, or for the exercise by the other party of any rights granted
hereunder, nor be liable to the other party for consequential damages under any
circumstances.

          7.09 Agency.  This MTA does not constitute either party hereto the
               ------
agent of the other party for any purpose whatsoever, nor does either party
thereto have the right or authority to assume, create, or incur any liability of
any kind, express, or implied, against or in the name or on behalf of the other
party.

IN WITNESS WHEREOF, the parties have executed and delivered this Agreement as of
the date written below.

                                             3-DIMENSIONAL PHARMACEUTICALS, INC.

                                             By:   /s/ F. Raymond Salemme
                                                  -----------------------------

                                             Dated: June 18, 1999
                                                    ---------------------------

                                             BIOCRYST PHARMACEUTICALS, INC.

                                             By:   /s/ Charles E. Bugg
                                                  -----------------------------

                                             Dated: June 18, 1999
                                                    ---------------------------

                                      G-5

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