Document:

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                                                                     Exhibit 4.1

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THIS WARRANT AND THE SHARES ISSUABLE UPON EXERCISE OF THIS WARRANT HAVE NOT BEEN
REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE "SECURITIES ACT"),
OR THE SECURITIES LAWS OF ANY STATE OF THE UNITED STATES OR ANY OTHER
JURISDICTION. THE SECURITIES REPRESENTED HEREBY MAY NOT BE OFFERED OR SOLD IN
THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT FOR THE SECURITIES UNDER
APPLICABLE SECURITIES LAWS UNLESS OFFERED, SOLD OR TRANSFERRED PURSUANT TO AN
AVAILABLE EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF THOSE LAWS.

                    Right to Purchase Shares of Common Stock

Date: October 18, 1999

                                 NETGENICS, INC.
                             STOCK PURCHASE WARRANT

         FOR VALUE RECEIVED, NETGENICS, INC., a Delaware corporation (the
"Company"), hereby grants, subject to the terms set forth below, INTERNATIONAL
BUSINESS MACHINES CORPORATION ("IBM" and each of its successors and assigns, a
"Holder"), a warrant (this "Warrant") to purchase the Warrant Shares at the
Purchase Price (as such terms are defined below):

         1. Certain Definitions. This Warrant is granted pursuant to and in
consideration of that certain Technical Services Agreement, of even date
herewith (the "Services Agreement"), among the Company and IBM. In addition to
the terms defined throughout this Warrant, the following terms shall have the
following meanings:

         (a) "Acquisition Transaction" shall mean (i) the sale, lease or other
transfer, in one or a series of transactions, of all or substantially all of the
Company's assets to any person or group (as such term is defined in Section
13(d)(3) of the Exchange Act) (a "Group"), or (ii) the consummation of any
transaction or series of transactions the result of which is that any person or
Group beneficially owns, directly or indirectly, 50% or more of the voting power
of the voting stock of the Company, provided, that transfers of assets of the
Company to any Affiliate shall not constitute an Acquisition Transaction
(subject to Section 5(b) below).

         (b) "Affiliate" shall mean any entity directly or indirectly controlled
by, controlling or under common control with another entity.

         (c) "Base Warrant Purchase Price" shall mean $5.00 per share of Common
Stock with respect to the Base Warrant Shares.

         (d)  "Base Warrant Shares" shall mean 150,000 shares of Common Stock.

         (e)  "Common Stock" shall mean the common shares of the Company.

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         (f) "Conversion Election" shall mean a writing delivered by IBM to the
Company evidencing IBM's election to convert the Services Converted Fee Amount
into the Services Fee Warrant Shares.

         (g) "Dilutive IPO" shall mean an IPO in which the per share offering
price is less than $3.00.

         (h) "IPO" shall mean a bona fide public offering and sale of Common
Stock pursuant to a registration statement filed under the Securities Act of
1933 and declared effective by the U.S. Securities and Exchange Commission.

         (i) "Piggyback Registration Right" shall mean a right of the Holder
under Section 7(a)(i) and (ii) hereof.

         (j) "Purchase Price" shall mean the Base Warrant Purchase Price with
respect to the Base Warrant Shares and the Services Fee Warrant Purchase Price
with respect to the Services Fee Warrant Shares, respectively.

         (k) "Registrable Securities" shall mean the Warrant Shares issued or
issuable with respect to the Warrant.

         (l) "Registration Expenses" shall mean all expenses incident to the
Company's performance of or compliance with the registration provisions of
Section 7 herein, including without limitation (i) all fees and expenses of
compliance with federal securities and state securities laws; (ii) all printing
expenses; (iii) all fees and disbursements of counsel for the Company; and (iv)
all fees and disbursements of accountants of the Company, but excluding (i)
underwriter's discounts relating to securities sold by the Selling Holder; (ii)
Commission and state securities laws filing fees relating to securities sold by
the Selling Holder; (iii) filings made with the NASD and counsel fees in
connection therewith; and (iv) fees and disbursements of counsel for the Selling
Holder.

         (m) "Services Agreement" shall mean the Technical Services Agreement,
of even date herewith, between the Company and IBM.

         (n) "Services Converted Fee Amount" shall mean one-third of the
Services Outstanding Fee Amount.

         (o) "Services Fee Warrant Purchase Price" shall mean $2.00 per share of
Common Stock with respect to the Services Fee Warrant Shares.

         (p) "Services Fee Warrant Shares" shall mean that number of shares of
Common Stock equal to the Services Converted Fee Amount divided by $1.

         (q) "Services Post-Conversion Fee Amount" shall mean (A) the Services
Outstanding Fee Amount, minus (B)(1) the Services Converted Fee Amount plus (2)
the dollar value of the services performed by the Company under the Services
Agreement (as determined pursuant to

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the Services Agreement and as mutually agreed to by IBM and the Company)
subsequent to the date on which the Conversion Election is delivered by IBM.

         (r) "Services Outstanding Fee Amount" shall mean the Services Total Fee
Amount minus the dollar value of the services performed by the Company under the
Services Agreement (as determined pursuant to the Services Agreement and as
mutually agreed to by IBM and the Company) at any point in time.

         (s)  "Services Total Fee Amount" shall mean $2,000,000.

         (t) "Warrant Shares" shall mean the Base Warrant Shares and the
Services Fee Warrant Shares, as may be adjusted from time to time pursuant to
Section 3 hereof.

         2. Exercise and Expiration of Warrant.

         (a) This Warrant is immediately exercisable, at any time or from time
to time on or after the date of initial issuance of this Warrant and shall
expire upon the earlier of the fifth anniversary of (i) the closing of an
Acquisition Transaction, or (ii) the closing of an IPO (such periods, the
"Exercise Period"), PROVIDED, that this Warrant shall only become effective with
respect to the Services Fee Warrant Shares upon the delivery of the Conversion
Election by IBM to the Company (it being understood and agreed that IBM may only
deliver one Conversion Election to the Company, unless otherwise agreed to by
IBM and the Company).

         (b) This Warrant may be exercised during the Exercise Period by the
Holder, in whole or in part, (i) by surrendering this Warrant at the principal
office of the Company, or at such other office or agency as the Company may
designate, accompanied by payment in full, in lawful money of the United States,
of the Purchase Price payable in respect of the number of Warrant Shares
purchased upon such exercise, (ii) if the Holder is effectuating a Cashless
Exercise (as defined in Section 14(a) hereof) pursuant to Section 14(a) hereof,
by delivery to the Company of a written notice of an election to effect a
Cashless Exercise for the Warrant Shares specified in the Exercise Agreement
(attached hereto), or (iii) with respect to the Services Fee Warrant Shares, by
IBM electing to apply the Services Post-Conversion Fee Amount toward the
Services Fee Warrant Purchase Price.

         (c) Each exercise of this Warrant shall be deemed to have been effected
immediately prior to the close of business on the day on which this Warrant
shall have been surrendered to the Company as provided in Section 2(b) above.

         (d) As soon as practicable after the exercise of this Warrant in full
or in part, the Company, at its expense, will cause to be issued in the name of,
and delivered to, the Holder (i) a certificate or certificates for the number of
full Warrant Shares to which the Holder shall be entitled upon such exercise
plus, in lieu of any fractional share to which the Holder would otherwise be
entitled, cash in an amount determined pursuant to Section 6 hereof; and (ii) in
case such exercise is in part only, a new warrant or warrants (dated the date
hereof) of like tenor, calling in the aggregate on the face or faces thereof for
the number of Warrant Shares equal (without giving effect to any adjustment
therein) to the number of such shares called for by the

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terms of this Warrant minus the number of such shares purchased by the Holder
upon such exercise. In the event IBM has delivered a Conversion Election to the
Company prior to such exercise, the new warrant or warrants shall specify the
number of new Warrant Shares that constitute Base Warrant Shares and Services
Fee Warrant Shares.

         3.   Adjustments.

         (a) General. The Purchase Price shall be subject to adjustment from
time to time pursuant to the terms of this Section 3.

         (b)  Diluting Issuances.

                  (i) Special Definitions. For purposes of this Section 3(b),
the following definitions shall apply: (A) "Option" shall mean rights, options
or warrants to subscribe for, purchase or otherwise acquire Common Stock or
Convertible Securities; (B) "Conversion Date" shall mean the first day of the
Exercise Period; (C) "Convertible Securities" shall mean any evidences of
indebtedness, shares or other securities directly or indirectly convertible into
or exchangeable for Common Stock; (D) "Additional Shares of Common Stock" shall
mean all shares of Common Stock issued (or, pursuant to Section 3(b)(iii) below,
deemed to be issued) by the Company after the Conversion Date other than (i)
shares of Common Stock issued upon exercise of the Warrants, (ii) shares of
Common Stock issued upon conversion of the preferred stock or warrants
outstanding as of the date hereof, (iii) up to an additional 4,000,000 shares of
Common Stock (as adjusted for stock splits, stock dividends and other
adjustments to the Company's Common Stock) issued before or after the date
hereof to employees, officers, directors or other persons performing services
for the Company pursuant to any stock option plan, stock purchase plan or
management incentive plan, agreement or arrangement approved by the Board of
Directors of the Company, (iv) the sale of convertible or other securities of
the Company (not to exceed a total investment of $15,000,000) within nine months
after the date hereof, or (v) shares of Common Stock issued in an IPO at a price
per share in excess of the Services Fee Warrant Purchase Price.

                  (ii) No Adjustment of Purchase Price. No adjustments to the
Purchase Price under this Section 3 shall be made unless the consideration per
share (determined pursuant to Section 3(b)(v)) for an Additional Share of Common
Stock issued or deemed to be issued by the Company is less than the Purchase
Price in effect on the date of, and immediately prior to, the issue of such
Additional Shares of Common Stock.

                  (iii) Issue of Securities Deemed Issue of Additional Shares of
Common Stock. If the Company at any time or from time to time after the
Conversion Date shall issue any Options or Convertible Securities or shall fix a
record date for the determination of holders of any class of securities entitled
to receive any such Options or Convertible Securities, then the maximum number
of shares of Common Stock (as set forth in the instrument relating thereto
without regard to any provision contained therein for a subsequent adjustment of
such number) issuable upon the exercise of such Options or, in the case of
Convertible Securities and Options therefor, the conversion or exchange of such
Convertible Securities, shall be deemed to be Additional Shares of Common Stock
issued as of the time of such issue or, in case such a record date shall have

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been fixed, as of the close of business on such record date, provided that
Additional Shares of Common Stock shall not be deemed to have been issued unless
the consideration per share (determined pursuant to Section 3(b)(v) hereof) of
such Additional Shares of Common Stock would be less than the Purchase Price in
effect on the date of and immediately prior to such issue, or such record date,
as the case may be, and provided further that in any such case in which
Additional Shares of Common Stock are deemed to be issued:

                           (A) No further adjustment in the Purchase Price shall
be made upon the subsequent issue of Convertible Securities or shares of Common
Stock upon the exercise of such Options or conversion or exchange of such
Convertible Securities;

                           (B) If such Options or Convertible Securities by
their terms provide, with the passage of time or otherwise, for any increase in
the consideration payable to the Company, upon the exercise, conversion or
exchange thereof, the Purchase Price computed upon the original issue thereof
(or upon the occurrence of a record date with respect thereto), and any
subsequent adjustments based thereon, shall, upon any such increase becoming
effective, be recomputed to reflect such increase insofar as it affects such
Options or the rights of conversion or exchange under such Convertible
Securities;

                           (C) Upon the expiration or termination of any
unexercised Option, the Purchase Price shall not be readjusted, but the
Additional Shares of Common Stock deemed issued as the result of the original
issue of such Option shall not be deemed issued for the purposes of any
subsequent adjustment of the Purchase Price;

                           (D) In the event of any change in the number of
shares of Common Stock issuable upon the exercise, conversion or exchange of any
Option or Convertible Security, including, but not limited to, a change
resulting from the anti-dilution provisions thereof, the Purchase Price then in
effect shall forthwith be readjusted to such Purchase Price as would have
obtained had the adjustment which was made upon the issuance of such Option or
Convertible Security not exercised or converted prior to such change been made
upon the basis of such change; and

                           (E) No readjustment pursuant to Clause (B) or (D)
above shall have the effect of increasing the Purchase Price to an amount which
exceeds the lower of (i) the Purchase Price on the original adjustment date, or
(ii) the Purchase Price that would have resulted from any issuances of
Additional Shares of Common Stock between the original adjustment date and such
readjustment date.

                  (iv) Adjustment of Purchase Price Upon Issuance of Additional
Shares of Common Stock. In the event the Company shall at any time after the
Conversion Date issue Additional Shares of Common Stock (including Additional
Shares of Common Stock deemed to be issued pursuant to Section 3(b)(iii), but
excluding shares issued as a dividend or distribution or upon a stock split or
combination as provided in Section 3(c)), without consideration or for a
consideration per share less than the Purchase Price in effect on the date of
and immediately prior to such issue, then and in such event, such Purchase Price
shall be reduced, concurrently with such issue, to a price (calculated to the
nearest cent) determined by multiplying such Purchase

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Price by a fraction, (A) the numerator of which shall be (1) the number of
shares of Common Stock outstanding immediately prior to such issue plus (2) the
number of shares of Common Stock which the aggregate consideration received or
to be received by the Company for the total number of Additional Shares of
Common Stock so issued would purchase at such Purchase Price; and (B) the
denominator of which shall be the number of shares of Common Stock outstanding
immediately prior to such issue plus the number of such Additional Shares of
Common Stock so issued; provided that, (i) for the purpose of this Section
3(b)(iv), all shares of Common Stock issuable upon exercise or conversion of
Options or Convertible Securities outstanding immediately prior to such issue
shall be deemed to be outstanding (other than shares excluded from the
definition of "Additional Shares of Common Stock" by virtue of Section
3(b)(i)(D)), and (ii) the number of shares of Common Stock deemed issuable upon
conversion of such outstanding Options and Convertible Securities shall not give
effect to any adjustments to the conversion price or conversion rate of such
Options or Convertible Securities resulting from the issuance of Additional
Shares of Common Stock that is the subject of this calculation.

                  (v) Determination of Consideration. For purposes of this
Section 3(b), the consideration received by the Company for the issue of any
Additional Shares of Common Stock shall be computed as follows:

                           (A) Cash and Property: Such consideration shall (I)
insofar as it consists of cash, be computed at the aggregate of cash received by
the Company, excluding amounts paid or payable for accrued interest or accrued
dividends; (II) insofar as it consists of property other than cash, be computed
at the fair market value thereof at the time of such issue, as determined in
good faith by the Board of Directors; and (III) in the event Additional Shares
of Common Stock are issued together with other shares or securities or other
assets of the Company for consideration which covers both, be the proportion of
such consideration so received, computed as provided in clauses (I) and (II)
above, as determined in good faith by the Board of Directors.

                           (B) Options and Convertible Securities. The
consideration per share received by the Company for Additional Shares of Common
Stock deemed to have been issued pursuant to Section 3(b)(iii), relating to
Options and Convertible Securities, shall be determined by dividing (x) the
total amount, if any, received or receivable by the Company as consideration for
the issue of such Options or Convertible Securities, plus the minimum aggregate
amount of additional consideration (as set forth in the instruments relating
thereto, without regard to any provision contained therein for a subsequent
adjustment of such consideration) payable to the Company upon the exercise of
such Options or the conversion or exchange of such Convertible Securities, or in
the case of Options for Convertible Securities, the exercise of such Options for
Convertible Securities and the conversion or exchange of such Convertible
Securities, by (y) the maximum number of shares of Common Stock (as set forth in
the instruments relating thereto, without regard to any provision contained
therein for a subsequent adjustment of such number) issuable upon the exercise
of such Options or the conversion or exchange of such Convertible Securities.

         (vi) Multiple Closing Dates. In the event the Company shall issue on
more than one date Additional Shares of Common Stock which are comprised of
shares of the same series or class of capital stock, and such issuance dates
occur within a period of no more than 60 days, then the

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Purchase Price shall be adjusted only once on account of such issuances, with
such adjustment to occur upon the final such issuance (but not later than ten
days prior to the end of the Exercise Period) and to give effect to all such
issuances as if they occurred on the date of the final such issuance.

          (c) Recapitalizations. If outstanding shares of the Company's Common
Stock shall be subdivided into a greater number of shares or a dividend in
Common Stock shall be paid in respect of Common Stock, the Purchase Price in
effect immediately prior to such subdivision or at the record date of such
dividend shall simultaneously with the effectiveness of such subdivision or
immediately after the record date of such dividend be proportionately reduced.
If outstanding shares of Common Stock shall be combined into a smaller number of
shares, the Purchase Price in effect immediately prior to such combination
shall, simultaneously with the effectiveness of such combination, be
proportionately increased.

          (d) Mergers, etc. If there shall occur any capital reorganization or
reclassification of the Company's Common Stock (other than a subdivision or
combination as provided for in Section 3(c) above), or any consolidation or
merger of the Company with or into another corporation, or a transfer of all or
substantially all of the assets of the Company, then, as part of any such
reorganization, reclassification, consolidation, merger or sale, as the case may
be, lawful provision shall be made so that the Holder of this Warrant shall have
the right thereafter to receive upon the exercise hereof the kind and amount of
shares of stock or other securities or property which such Holder would have
been entitled to receive if, immediately prior to any such reorganization,
reclassification, consolidation, merger or sale, as the case may be, such Holder
had held the number of shares of Common Stock which were then purchasable upon
the exercise of this Warrant. In any such case, appropriate adjustment (as
reasonably determined in good faith by the Board of Directors of the Company)
shall be made in the application of the provisions set forth herein with respect
to the rights and interests thereafter of the Holder of this Warrant, such that
the provisions set forth in this Section 3 (including provisions with respect to
adjustment of the Purchase Price) shall thereafter be applicable, as nearly as
is reasonably practicable, in relation to any shares of stock or other
securities or property thereafter deliverable upon the exercise of this Warrant.

          (e) Adjustment in Number of Warrant Shares. When any adjustment is
required to be made in the Purchase Price, the number of Warrant Shares
purchasable upon the exercise of this Warrant shall be changed to the number
determined by dividing (i) an amount equal to the number of shares issuable upon
the exercise of this Warrant immediately prior to such adjustment, multiplied by
the Purchase Price in effect immediately prior to such adjustment, by (ii) the
Purchase Price in effect immediately after such adjustment.

          (f) Certificate of Adjustment. When any adjustment is required to be
made pursuant to this Section 3, the Company shall promptly mail to the Holder a
certificate setting forth the Purchase Price after such adjustment and setting
forth a brief statement of the facts requiring such adjustment. Such certificate
shall also set forth the kind and amount of stock or other securities or
property into which this Warrant shall be exercisable following such adjustment.

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          (g) Adjustments for Non-Stock Dividends and Distributions. In the
event that the Company shall issue or pay to holders of Common Stock a dividend
or other distribution payable other than in securities of the Company, then and
in each such event provision shall he made so that Holder shall receive upon
exercise of this Warrant, in addition to the Warrant Shares issued upon
exercise, the dividend or other distribution which Holder would have received if
it had been the holder of such Warrant Shares at the time of such dividend or
other distribution.

         (h)  Other Notices.  In case at any time:

                (i) the Company shall declare any dividend upon the Common Stock
payable in shares of stock of any class or make any other distribution (other
than dividends or distributions payable in cash out of retained earnings
consistent with the Company's past practices with respect to declaring dividends
and making distributions) to the holders of the Common Stock;

                (ii) the Company shall offer for subscription pro rata to the
holders of the Common Stock any additional shares of stock of any class or other
rights;

                (iii) there shall be any capital reorganization of the Company,
or reclassification of the Common Stock, or consolidation or merger of the
Company with or into, or sale of all or substantially all of its assets to,
another corporation or entity; or

                (iv) there shall be a voluntary or involuntary dissolution,
liquidation or winding-up of the Company;

then, in each such case, the Company shall give to the Holder (a) notice of the
date on which the books of the Company shall close or a record shall be taken
for determining the holders of Common Stock entitled to receive any such
dividend, distribution, or subscription rights or for determining the holders of
Common Stock entitled to vote in respect of any such reorganization,
reclassification, consolidation, merger, sale, dissolution, liquidation or
winding-up and (b) in the case of any such reorganization, reclassification,
consolidation, merger, sale, dissolution, liquidation or winding-up, notice of
the date (or, if not then known, a reasonable estimate thereof by the Company)
when the same shall take place. Such notice shall also specify the date on which
the holders of Common Stock shall be entitled to receive such dividend,
distribution, or subscription rights or to exchange their Common Stock for stock
or other securities or property deliverable upon such reorganization,
reclassification, consolidation, merger, sale, dissolution, liquidation, or
winding-up, as the case may be. Such notice shall be given at least thirty (30)
days prior to the record date or the date on which the Company's books are
closed in respect thereto. Failure to give any such notice or any defect therein
shall not affect the validity of the proceedings referred to in clauses (i),
(ii), (iii) and (iv) above.

           (i) Certain Events. If, at any time during the Exercise Period, any
event occurs of the type contemplated by the adjustment provisions of this
Section 3 but not expressly provided for by such provisions, the Company will
give notice of such event , and the Company's Board of Directors will make an
appropriate adjustment in the Exercise Price and the number of shares of Common
Stock acquirable upon exercise of this Warrant so that the rights of the Holder
shall be neither enhanced nor diminished by such event.

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         (j) Special Exclusive Adjustment for Services Fee Warrant Shares in the
Event of a Dilutive IPO. In the event that IBM has delivered a Conversion
Election prior to the date on which the Company completes a Dilutive IPO, then
upon the closing of the Dilutive IPO (i) the number of Services Fee Warrant
Shares shall be adjusted by multiplying the Services Fee Warrant Shares by a
fraction, the numerator of which is 3 and the denominator of which is the per
share offering price in the Dilutive IPO, and (ii) the Services Fee Warrant
Purchase Price shall be adjusted by multiplying the Services Fee Warrant
Purchase Price by a fraction, the numerator of which is the per share offering
price in the Dilutive IPO and the denominator of which is 3. It is understood
and agreed that this adjustment to the Services Fee Warrant Shares and the
Services Fee Warrant Purchase Price shall be the exclusive adjustment to such
shares and such price in the event of a Dilutive IPO, notwithstanding the other
provisions of this Section 3.

         4. Acquisition Transaction. If the Company undertakes an Acquisition
Transaction then, simultaneously with and as a condition to the Acquisition
Transaction, the Company shall, at the Company's election, either (i) cause the
Company Acquiror (as defined below) to assume this Warrant and cause provision
to be made so that the Holder shall thereafter be entitled to receive, upon
exercise of this Warrant, the Warrant Shares, whereupon the Company shall be
released from this Warrant, or (ii) cause the Company Acquiror to pay the
Warrant Value (as defined below) to the Holder upon consummation of the
Acquisition Transaction. If this Warrant becomes exercisable by reason of an
Acquisition Transaction and the Company does not cause the Company Acquiror to
pay the Warrant Value to the Holder, this Warrant shall remain outstanding in
accordance with its terms and all references herein to the "Company" shall
thereafter be deemed to apply to the Company Acquiror and all references herein
to the "Warrant Shares" shall thereafter be deemed to apply to the common stock
of the Company Acquiror. "Company Acquiror" shall mean the Company or other
entity, as applicable, surviving the Acquisition Transaction. In the event of
the consummation of any transaction or series of transactions the result of
which is that any person or Group beneficially owns, directly or indirectly, 50%
or more of the voting power of the voting stock of the Company (such transaction
or transactions, a "Stock Acquisition"), "Warrant Value" shall mean the value of
this Warrant calculated as if the Holder had exercised this Warrant at such time
pursuant to Section 14(a) hereof with the Market Price equal to the per share
consideration paid in the Stock Acquisition. Otherwise, "Warrant Value" shall
mean the fair market value of this Warrant immediately prior to the closing of
the Acquisition Transaction, as determined by an investment banking firm of
established national reputation selected by the Holder and stated in a written
opinion delivered to the Company and the Holder. The fees and expenses of such
investment banking firm shall be shared equally by the Company and the Holder
and its determination of the Warrant Value shall be conclusive and binding on
all parties in the absence of fraud or manifest error.

         5.   Acquisition or IPO by Affiliate.

         (a) IPO by Affiliate. If, prior to an IPO, the Company transfers all or
substantially all of its assets to any Affiliate and the Affiliate subsequently
undertakes a transaction which would constitute an IPO (an "Affiliate IPO") if
undertaken by the Company, then, simultaneously with

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and as a condition to the Affiliate IPO, the Affiliate shall assume this
Warrant, provision shall be made so that the Holder shall be entitled to
receive, upon exercise of this Warrant, shares of stock or other securities or
property of the Affiliate to which it is entitled under this Warrant, and the
Company shall be released from this Warrant.

          (b) Acquisition by Affiliate. If, prior to an Acquisition Transaction,
the Company transfers all or substantially all of its assets to an Affiliate and
the Affiliate subsequently undertakes a transaction which would constitute an
Acquisition Transaction (an "Affiliate Acquisition") if undertaken by the
Company, then, simultaneously with and as a condition to the Affiliate
Acquisition, the Company shall, at the Company's election, either (i) cause the
Affiliate Acquiror (as defined below) to assume this Warrant and cause provision
to be made so that the Holder shall thereafter be entitled to receive, upon
exercise of this Warrant, the Warrant Shares, whereupon the Company shall be
released from this Warrant, or (ii) cause the Affiliate Acquiror to pay the
Warrant Value (as defined above, except that references to Acquisition
Transaction shall mean Affiliate Acquisition) to the Holder upon consummation of
the Affiliate Acquisition. If this Warrant becomes exercisable by reason of a
Affiliate Acquisition and the Affiliate does not cause the Affiliate Acquiror to
pay the Warrant Value to the Holder, this Warrant shall remain outstanding in
accordance with its terms and all references herein to the "Company" shall
thereafter be deemed to apply to the Affiliate Acquiror and all references
herein to the "Warrant Shares" shall thereafter be deemed to apply to the common
stock of the Affiliate Acquiror. "Affiliate Acquiror" shall mean the Affiliate
or other entity, as applicable, surviving the Affiliate Acquisition.

         6. Fractional Shares. The Company shall not be required upon the
exercise of this Warrant to issue any fractional shares, but shall make an
adjustment therefor in cash on the basis of the fair market value per share of
Common Stock, as determined in good faith by the Company's Board of Directors.

         7.  Registration Rights.

         (a)  Piggyback Registration

                  (i) Participation - IPO. If the Company elects to file a
registration statement under the Securities Act in connection with an IPO, the
Company shall give written notice thereof to the Holder at least twenty business
days before filing. The Holder shall have the right to participate in the IPO on
a pro rata basis with any other holders entitled to participate in such offering
upon the giving of notice to the Company within ten business days of receipt by
it of notice from the Company. If the Holder notifies the Company of its intent
to exercise such Piggyback Registration Right, subject to Section 7(a)(iii), the
Company shall include in such registration statement such number of shares of
Registrable Securities equal to the same percentage of the total number of
Registrable Securities issuable upon exercise of the Warrant as the number of
shares of the other holders' Common Stock to be registered bears to such other
holders' aggregate ownership of Common Stock. Such Registrable Securities shall
be included in the underwriting for the IPO on the same terms and conditions as
the securities otherwise being sold in such offering.

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                  (ii) Participation - Other Offerings. If the Company elects to
file a registration statement under the Securities Act covering the offer and
sale of any Common Stock (or equity securities converted into Common Stock) in
connection with any public offering after the IPO (other than a registration
statement on Form S-8 or Form S-4, or their successors, or any other form for a
similar limited purpose, or any registration statement covering only securities
proposed to be issued in exchange for securities or assets of another
corporation), the Company shall give written notice thereof to the Holder at
least twenty business days before filing. The Holder shall have a Piggyback
Registration Right to participate in such offering on a pro rata basis with the
Company and any other Holders upon the giving of notice to the Company within
ten business days of receipt by it of notice from the Company. If the Holder
notifies the Company of its intent to exercise such Piggyback Registration
Right, subject to Section 7(a)(iii), the Company shall include in such
registration statement such number of shares of Registrable Securities equal to
the percentage of the total number of Warrant Shares held by the Holder
multiplied by the number of shares proposed to be registered in the offering.
Such Registrable Securities shall be included in the underwriting for the public
offering on the same terms and conditions as the securities otherwise being sold
in such offering.

                  (iii) Underwriter's Cutback. If, in the opinion of the
managing underwriter of such offering the inclusion of all of the shares of
Registrable Securities and other Common Stock requested to be registered would
be inappropriate, then the number of shares of Registrable Securities and other
Common Stock to be included in the offering shall be reduced, with the
participation in such offering to be in the following order of priority: (1)
first, securities to be issued by the Company shall be included, and (2) second,
any other Common Stock required to be included pursuant to any demand
registration right granted to such other Holder of Common Stock shall be
included, and (3) third Registrable Securities and any other Common Stock
requested to be included, on a pro rata basis, shall be included.

                  (iv) Registrant Controls. The Company may decline to file a
Registration Statement after giving notice to any Holder, or withdraw a
Registration Statement after filing and after such notice, but prior to the
effectiveness thereof, provided that such registrant shall promptly notify each
Holder of Registrable Securities in writing of any such action and provided
further that such registrant shall bear all reasonable expenses incurred by such
Holder of Registrable Securities or otherwise in connection with such withdrawn
Registration Statement.

                  (vi) Underwriting Agreement. In connection with any
registration under this Section 7(a) involving an underwriting, the Company
shall not be required to include any Registrable Shares in such registration
unless the Holder accepts the terms of the underwriting as determined by the
underwriters selected by the Company (provided that such terms must be
consistent with this Agreement and provided, further, that any inability of the
Holder to agree with the underwriters shall not restrict the ability of the
Company to proceed with the registration).

         (b)  Indemnification.

                  (i) Indemnification by the Company. The Company agrees to
indemnify and hold harmless any Holder of Registrable Securities which has
included Registrable Securities in

                                       11
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a registration statement, its officers, directors and agents and each Person, if
any, who controls such Holder within the meaning of Section 15 of the Securities
Act or Section 20 of the Securities Exchange Act of 1934, as amended (the
"Exchange Act") from and against any and all losses, claims, damages,
liabilities and expenses (including reasonable costs of investigation) arising
out of or based upon any untrue statement or alleged untrue statement of a
material fact contained in any registration statement or final prospectus
relating to the Registrable Securities or in any amendment or supplement thereto
or in any preliminary prospectus, or arising out of or based upon any omission
or alleged omission to state therein a material fact required to be stated
therein or necessary to make the statements therein not misleading, except
insofar as such losses, claims, damages, liabilities or expenses arise out of,
or are based upon, any such untrue statement or omission based upon information
furnished in writing to Company by the Holder of the Registrable Securities or
on such Holder's behalf expressly for use therein; provided, that with respect
to any untrue statement or omission made in any preliminary prospectus, the
indemnity agreement contained in this paragraph shall not apply to the extent
that any such loss, claim, damage, liability or expense results from the fact
that a current copy of the prospectus was not sent or given to the person
asserting any such loss, claim, damage, liability or expense at or prior to the
written confirmation of the sale of the Registrable Securities concerned if it
is determined that it was the responsibility of the Holder of such Registrable
Securities to provide such person with a current copy of the prospectus and such
current copy of the prospectus would have cured the defect giving rise to such
loss, claim, damage, liability or expense. The Company also agrees to indemnify
any underwriters of the Registrable Securities, their officers and directors and
each person who controls such underwriters on substantially the same basis as
that of the indemnification of the Holder of such Registrable Securities
provided in this Section 7(b).

               (ii) Indemnification by the Holder of Registrable Securities. The
Holder of Registrable Securities, to the extent it is selling Registrable
Securities ("Selling Holder"), agrees to indemnify and hold harmless the
Company, its directors and officers and each Person, if any, who controls the
Company within the meaning of either Section 15 of the Securities Act or Section
20 of the Exchange Act to the same extent as the foregoing indemnity from the
Company to the Selling Holder, but only with respect to information furnished in
writing by the Selling Holder or on the Selling Holder's behalf expressly for
use in any registration statement or final prospectus relating to the
Registrable Securities (or any amendment or supplement thereto, or any
preliminary prospectus) which contained an untrue statement or alleged untrue
statement of a material fact or omitted or allegedly omitted to state therein a
material fact required to be stated therein or necessary to make the statements
therein not misleading . In case any action or proceeding shall be brought
against the Company or its directors or officers, or any such controlling
Person, in respect of which indemnity may be sought against such Selling Holder,
such Selling Holder shall have the rights and duties given to the Company, and
the Company or its directors or officers or such controlling Person shall have
the rights and duties given to such Selling Holder, by the preceding subsection.
The Selling Holder also agrees to indemnify and hold harmless the underwriters
on substantially the same basis of that of the indemnification of the Company
provided in the preceding subsection.

                                       12
<PAGE>   13

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         (c) Contribution. If the indemnification provided for in Section 7(b)
hereof is unavailable to the Company, the Selling Holder or the underwriters in
respect of any losses, claims, damages, liabilities, expenses or judgments
referred to herein, then each such indemnifying party, in lieu of indemnifying
such indemnified party, shall contribute to the amount paid or payable by such
indemnified party as a result of such losses, claims, damages, liabilities,
expenses and judgments (i) as between the Company and the Selling Holder on the
one hand and the underwriters on the other, in such proportion as is appropriate
to reflect the relative benefits received by the Company and the Selling Holder
on the one hand and the underwriters on the other from the offering of the
Registrable Securities, or if such allocation is not permitted by applicable
law, in such proportion as is appropriate to reflect not only such relative
benefits but also the relative fault of the Company and the Selling Holder on
the one hand and of the underwriters on the other in connection with the
statements or omissions which resulted in such losses, claims, damages,
liabilities, expenses or judgments, as well as any other relevant equitable
considerations and (ii) as between the Company on the one hand and each Selling
Holder on the other, in such proportion as is appropriate to reflect the
relative fault of the Company and of each Selling Holder in connection with such
statements or omissions, as well as any other relevant equitable considerations.
The relative benefits received by the Company and the Selling Holder on the one
hand and the underwriters on the other shall be deemed to be in the same
proportion as the total proceeds from the offering (net of underwriting
discounts and commissions but before deducting expenses) received by the Company
and the Selling Holder bear to the total underwriting discounts and commissions
received by the underwriters, in each case as set forth in the table on the
cover page of the prospectus. The relative fault of the Company on the one hand
and of each Selling Holder on the other shall be determined by reference to,
among other things, whether the untrue or alleged untrue statement of a material
fact or the omission or alleged omission to state a material fact relates to
information supplied by such party, and the party's relative intent, knowledge,
access to information and opportunity to correct or prevent such statement or
omission.

         The Company and the Holder agree that it would not be just and
equitable if contribution pursuant to this Section 7(c) were determined by pro
rata allocation or by any other method of allocation which does not take account
of the equitable considerations referred to in the immediately preceding
paragraph. The amount paid or payable by an indemnified party as a result of the
losses, claims, damages, liabilities, expenses or judgments referred to in the
immediately preceding paragraph shall be deemed to include, subject to the
limitations set forth above, any legal or other expenses reasonably incurred by
such indemnified party in connection with investigating or defending any such
action or claim. Notwithstanding the provisions of this Section 7(c), no
underwriter shall be required to contribute any amount in excess of the amount
by which the total price at which the Registrable Securities underwritten by it
and distributed to the public were offered to the public exceeds the amount of
any damages which such underwriter has otherwise been required to pay by reason
of such untrue or alleged untrue statement or omission or alleged omission, and
no Selling Holder shall be required to contribute any amount in excess of the
amount by which the total price at which the Registrable Securities of such
Selling Holder were offered to the public exceeds the amount of any damages
which such Selling Holder has otherwise been required to pay by reason of such
untrue or alleged untrue statement or omission or alleged omission. No person
guilty of fraudulent misrepresentation (within the

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meaning of Section 11(f) of the Securities Act) shall be entitled to
contribution from any person who was not guilty of such fraudulent
misrepresentation.

         (d)  Registration Expenses.

                  (i) Piggyback Registrations. The Company shall bear all
Registration Expenses incurred in connection with Piggyback Registrations.

                  (ii) Expenses of Registrant. The Company will, in any event,
pay its internal expenses (including, without limitation, all salaries and
expenses of its officers and employees performing legal or accounting duties),
the expense of any annual audit, the fees and expenses incurred in connection
with any listing of the securities to be registered on a securities exchange,
and the fees and expenses of any person, including special experts, retained by
the Company.

         8.   Assignment of Registration Rights.

         The rights of the Holders hereunder, including the right to have the
Company register Registrable Securities pursuant to this Agreement, shall be
automatically assignable by each Holder to any transferee of all or any portion
of the Warrant or the Registrable Securities if: (i) the Holder agrees in
writing with the transferee or assignee to assign such rights, and a copy of
such agreement is furnished to the Company after such assignment, (ii) the
Company is furnished with written notice of (a) the name and address of such
transferee or assignee, and (b) the securities with respect to which such
registration rights are being transferred or assigned, (iii) following such
transfer or assignment, the further disposition of such securities by the
transferee or assignee is restricted under the Securities Act and applicable
state securities laws, (iv) the transferee or assignee agrees in writing for the
benefit of the Company to be bound by all of the provisions contained herein,
and (v) such transfer shall have been made in accordance with the applicable
requirements of the Warrant.

         9.   Representations.

         (a) By the Holder. By accepting this Warrant, the Holder hereof
represents that this Warrant is acquired for the Holder's own account for
investment purposes and not with a view to any offering or distribution and that
the Holder has no present intention of selling or otherwise disposing of the
Warrant or any portion hereof or the underlying shares of Common Stock in
violation of applicable securities laws.

         (b)  By the Company.

                  (i) Neither the Company, nor any of its affiliates, nor any
person acting on its or their behalf, has directly or indirectly made any offers
or sales of any security or solicited any offers to buy any security under
circumstances that would require registration, or the filing of a prospectus
qualifying the distribution, of this Warrant being issued hereby under the
Securities Act or cause the issuance of this Warrant to be integrated with any
prior offering of securities of the Company for purposes of the Securities Act.

                                       14
<PAGE>   15

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                  (ii) The Company represents and warrants that as of the date
hereof, it has outstanding 28,569,839 shares of Common Stock, calculated on a
fully diluted basis, giving effect to the conversion of all options, warrants,
rights and other securities convertible into, or exchangeable for, Common Stock.

         10. Certain Agreements of the Company. The Company hereby covenants and
agrees as follows:

          (a) Shares to be Fully Paid. All Warrant Shares will, upon issuance in
accordance with the terms of this Warrant, be validly issued, fully paid, and
nonassessable and free from all taxes, liens, claims and encumbrances.

           (b) Authorization of Shares. During the Exercise Period, the Company
shall at all times have authorized a sufficient number of shares of Common
Stock, free from preemptive rights and from any other restrictions imposed by
the Company without the consent of the Holder, to provide for the exercise in
full of this Warrant.

           (c) Listing. The Company shall promptly secure the listing of the
shares of Common Stock issuable upon exercise of this Warrant upon each national
securities exchange or automated quotation system, if any, upon which shares of
Common Stock are then listed or become listed (subject to official notice of
issuance upon exercise of this Warrant) and shall maintain, so long as any other
shares of Common Stock shall be so listed, such listing of all shares of Common
Stock from time to time issuable upon the exercise of this Warrant; and the
Company shall so list on each national securities exchange or automated
quotation system, as the case may be, and shall maintain such listing of, any
other shares of capital stock of the Company issuable upon the exercise of this
Warrant if and so long as any shares of the same class shall be listed on such
national securities exchange or automated quotation system.

          (d) Certain Actions Prohibited. The Company will not, by amendment of
its charter or through any reorganization, transfer of assets, consolidation,
merger, dissolution, issue or sale of securities, or any other voluntary action,
avoid or seek to avoid the observance or performance of any of the terms to be
observed or performed by it hereunder, but will at all times in good faith
assist in the carrying out of all the provisions of this Warrant and in the
taking of all such action as may reasonably be requested by the Holder of this
Warrant in order to protect the exercise privilege of the Holder of this Warrant
against dilution or other impairment, consistent with the tenor and purpose of
this Warrant. Without limiting the generality of the foregoing, the Company will
take all such actions as may be necessary or appropriate in order that the
Company may validly and legally issue fully paid and nonassessable shares of
Common Stock upon the exercise of this Warrant.

           (e) Successors and Assigns. This Warrant will be binding upon any
entity succeeding to the Company by merger, consolidation, or acquisition of all
or substantially all of the Company's assets.

           (f) Blue Sky Laws. The Company shall, on or before the date of
issuance of any Warrant Shares, take such actions as the Company shall
reasonably determine are necessary to qualify the

                                       15
<PAGE>   16

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Warrant Shares for, or obtain exemption for the Warrant Shares for, sale to the
Holder of this Warrant upon the exercise hereof under applicable securities or
"blue sky" laws of the states of the United States, and shall provide evidence
of any such action so taken to the Holder of this Warrant prior to such date;
provided, however, that the Company shall not be required to qualify as a
foreign corporation or file a general consent to service of process in any such
jurisdiction.

         (g) No Integrated Offerings. The Company shall not make any offers or
sales of any security under circumstances that would require registration, or
qualification of the distribution, of the Warrant under the Securities Act or
cause the issuance of this Warrant to be integrated with any other offering of
securities by the Company for purposes of the Securities Act.

         11.  Transfer,  Exchange, Redemption  and  Replacement of Warrant.

           (a) Transferability. This Warrant and the rights granted to the
Holder hereof are transferable, in whole or in part, upon surrender of this
Warrant, together with a properly executed assignment in the form attached
hereto, at the office or agency of the Company referred to in Section 12 below.
Until due presentment for registration of transfer on the books of the Company,
the Company may treat the registered Holder hereof as the owner hereof for all
purposes, and the Company shall not be affected by any notice to the contrary.

         (b) Warrant Exchangeable for Different Denominations. This Warrant is
exchangeable, upon the surrender hereof by the Holder hereof at the office or
agency of the Company referred to in Section 12 below, for new Warrants of like
tenor of different denominations representing in the aggregate the right to
purchase the number of shares of Common Stock which may be purchased hereunder,
each of such new Warrants to represent the right to purchase such number of
shares as shall be designated by the Holder hereof at the time of such
surrender.

           (c) Replacement of Warrant. Upon receipt of evidence reasonably
satisfactory to the Company of the loss, theft, destruction, or mutilation of
this Warrant and, in the case of any such loss, theft, or destruction, upon
delivery of an indemnity agreement reasonably satisfactory in form and amount to
the Company, or, in the case of any such mutilation, upon surrender and
cancellation of this Warrant, the Company, at its expense, will execute and
deliver, in lieu thereof, a new Warrant of like tenor.

           (d) Cancellation; Payment of Expenses. Upon the surrender of this
Warrant in connection with any transfer, exchange, or replacement as provided in
this Section 11, this Warrant shall be promptly canceled by the Company. The
Company shall pay all taxes (other than securities transfer taxes) and all other
expenses (other than legal expenses, if any, incurred by the Holder or
transferees) and charges payable in connection with the preparation, execution,
and delivery of Warrant pursuant to this Section 11. The Company shall indemnify
and reimburse the Holder of this Warrant for all costs and expenses (including
legal fees) incurred by such Holder in connection with the enforcement of its
rights hereunder.

           (e) Warrant Register. The Company shall maintain, at its principal
executive offices (or such other office or agency of the Company as it may
designate by notice to the Holder hereof),

                                       16
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a register for this Warrant, in which the Company shall record the name and
address of the person in whose name this Warrant has been issued, as well as the
name and address of each transferee and each prior owner of this Warrant.

          (f) Exercise or Transfer Without Registration. If, at the time of the
surrender of this Warrant in connection with any exercise, transfer, or exchange
of this Warrant, this Warrant (or, in the case of any exercise, the Warrant
Shares issuable hereunder), shall not be registered under the Securities Act and
under applicable state securities or blue sky laws, the Company may require, as
a condition of allowing such exercise, transfer, or exchange, (i) that the
Holder or transferee of this Warrant, as the case may be, furnish to the Company
a written opinion of counsel (which opinion shall be in form, substance and
scope customary for opinions of counsel in comparable transactions) to the
effect that such exercise, transfer, or exchange may be made without
registration under the Securities Act and under applicable state securities or
blue sky laws, (ii) that the Holder or transferee execute and deliver to the
Company an investment letter in form and substance acceptable to the Company and
(iii) that the transferee be an "accredited investor" as defined in Rule 501(a)
promulgated under the Securities Act; provided that no such opinion, letter, or
status as an "accredited investor" shall be required in connection with a
transfer pursuant to Rule 144 under the Securities Act.

         12. Notices. Any notices required or permitted to be given under the
terms of this Warrant shall be sent by certified or registered mail (return
receipt requested) or delivered personally or by courier or by confirmed
telecopy, and shall be effective five days after being placed in the mail, if
mailed, or upon receipt or refusal of receipt, if delivered personally or by
courier, or by confirmed telecopy, in each case addressed to a party. The
addresses for such communications shall be:

               If to the Company:

                  NetGenics, Inc.
                  1717 East Ninth Street
                  Cleveland, OH 44114

If to the Holder, at such address as such Holder shall have provided in writing
to the Company, or at such other address as such Holder furnishes by notice
given in accordance with this Section 12.

         13. Governing Law; Jurisdiction. This Warrant shall be governed by and
construed in accordance with the laws of the State of New York applicable to
contracts made and to be performed in New York. The Company irrevocably consents
to the exclusive jurisdiction of the United States federal courts and state
courts located in the State of New York in the County of Westchester in any suit
or proceeding based on or arising under this Warrant and irrevocably agrees that
all claims in respect of such suit or proceeding may be determined in such
courts. The Company irrevocably waives any objection to the laying of venue and
the defense of an inconvenient forum to the maintenance of such suit or
proceeding. The Company further agrees that service of process upon the Company
mailed by certified or registered mail shall be deemed in every respect
effective service of process upon the Company in any such suit or proceeding.

                                       17
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Nothing herein shall affect the holder's right to serve process in any other
manner permitted by law. The Company agrees that a final non-appealable judgment
in any such suit or proceeding shall be conclusive and may be enforced in other
jurisdictions by suit on such judgment or in any other lawful manner.

     14.  Miscellaneous.

         (a) Cashless Exercise. Notwithstanding anything to the contrary
contained in this Warrant, this Warrant may be exercised at any time during the
Exercise Period, by presentation and surrender of this Warrant to the Company at
its principal executive offices with a written notice of the holder's intention
to effect a cashless exercise, including a calculation of the number of shares
of Common Stock to be issued upon such exercise in accordance with the terms
hereof (a "Cashless Exercise"). In the event of a Cashless Exercise, in lieu of
paying the Exercise Price in cash, the Holder shall surrender this Warrant for
that number of shares of Common Stock determined by multiplying the number of
Warrant Shares to which it would otherwise be entitled by a fraction, the
numerator of which shall be the difference between the then current Market Price
of a share of the Common Stock on the date of exercise and the Exercise Price,
and the denominator of which shall be the then current Market Price per share of
Common Stock. "Market Price," as of any date, means the following: (i) the
average of the closing sale prices for the shares of Common Stock as reported on
the principal trading market for the Common Stock for the five (5) consecutive
trading days immediately preceding such date, or if no sale price is so reported
for such period, the last bid price for such period, or (ii) if the foregoing
does not apply, the last sale price of such security in the over-the-counter
market on the pink sheets or bulletin board for such security on the last
trading day immediately preceding such date, or if no sale price is so reported
for such security, the average of the last bid and ask price for such security
on the last trading day immediately preceding such date,, or (iii) if market
value cannot be calculated as of such date on any of the foregoing bases, the
Market Price shall be the average fair market value as reasonably determined by
an investment banking firm selected by the Company and reasonably acceptable to
the Holder, with the costs of the appraisal to be borne by the Company.

         (b) Amendments. This Warrant and any provision hereof may only be
amended by an instrument in writing signed by the Company and the Holder hereof.

         (c) U.S. Dollars. All references in this Warrant to "dollars" or "$"
shall mean the U.S. dollar.

         (d) Descriptive Headings. The descriptive headings of the several
Sections of this Warrant are inserted for purposes of reference only, and shall
not affect the meaning or construction of any of the provisions hereof.

         (e) Business Day. For purposes of this Warrant, the term "business day"
means any day, other than a Saturday or Sunday or a day on which banking
institutions in New York, New York are authorized or obligated by law,
regulation or executive order to close.

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         IN WITNESS WHEREOF, the Company has caused this Warrant to be signed by
its duly authorized officer.

NETGENICS, INC.

By: /S/ MANUEL J. GLYNIAS
    ---------------------
    Name:  Manuel J. Glynias
    Title:  President and Chief Executive Officer

WITNESS:_/S/ ELIZABETH SUMP-KLEINHENZ
-------------------------------------

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                           FORM OF EXERCISE AGREEMENT
                           --------------------------

         (To be Executed by the Holder in order to Exercise the Warrant)

To:      Netgenic, Inc.
         1717 East Ninth Street
         Cleveland, OH 44114

         The undersigned hereby irrevocably exercises the right to purchase
_____________ shares of the Common Stock of Netgenics, Inc. (the "Company"),
evidenced by the attached Warrant, and herewith makes payment of the Exercise
Price with respect to such shares in full, all in accordance with the conditions
and provisions of said Warrant.

      (i) The undersigned agrees not to offer, sell, transfer or otherwise
dispose of any Common Stock obtained on exercise of the Warrant, except under
circumstances that will not result in a violation of the Securities Act of 1933,
as amended, or any state securities laws, and agrees that the following legend
may be affixed to the stock certificate for the Common Stock hereby subscribed
for if resale of such Common Stock is not registered or if Rule 144 is
unavailable:

     THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED
     UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR THE SECURITIES LAWS OF ANY
     STATE OF THE UNITED STATES. THE SECURITIES REPRESENTED HEREBY MAY NOT BE
     OFFERED OR SOLD IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT FOR
     THE SECURITIES UNDER APPLICABLE SECURITIES LAWS UNLESS OFFERED, SOLD OR
     TRANSFERRED PURSUANT TO AN AVAILABLE EXEMPTION FROM THE REGISTRATION
     REQUIREMENTS OF THOSE LAWS.

      (ii) The undersigned requests that stock certificates for such shares be
issued, and a Warrant representing any unexercised portion hereof be issued,
pursuant to the Warrant in the name of the Holder and delivered to the
undersigned at the address set forth below:

Dated:
      -----------------

----------------------------
     Signature of Holder

-------------------------------------
     Name of Holder (Print)

Address:

-------------------------------------

-------------------------------------

-------------------------------------

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                               FORM OF ASSIGNMENT

      FOR VALUE RECEIVED, the undersigned hereby sells, assigns, and transfers
all the rights of the undersigned under the within Warrant, with respect to the
number of shares of Common Stock covered thereby set forth hereinbelow, to:

Name of Assignee         Address                  No of Shares

, and hereby irrevocably constitutes and appoints ______________________________
as agent and attorney-in- fact to transfer said Warrant on the books of the
within-named corporation, with full power of substitution in the premises.

Dated:
       ---------------------, ----

In the presence of

------------------
Name:

Signature:
           -----------------------

Title of Signing Officer or Agent (if any):
                                           ------------------------

Address:
         --------------------
         --------------------

Note: The above signature should correspond exactly with the name on the face of
the within Warrant.

                                       21<PAGE>   1
                                                                    Exhibit 10.1

                          D&O INDEMNIFICATION AGREEMENT
                          -----------------------------

         This D&O Indemnification Agreement, dated as of ___________ ___, 200_
(this "Agreement"), is made by and between NetGenics, Inc., a Delaware
corporation (the "Company"), and __________________ ("Indemnitee").

                                    RECITALS

         A. It is important to the Company to attract and retain as directors
and officers the most capable persons reasonably available.

         B. Indemnitee is a director and/or officer of the Company.

         C. Both the Company and Indemnitee recognize the increased risk of
litigation and other claims being asserted against directors and officers of
companies in today's environment.

         D. The Company's Certificate of Incorporation and/or By-laws (the
"Constituent Documents") provide that the Company will indemnify its directors
and officers and will advance expenses in connection therewith, and Indemnitee's
willingness to serve as a director and/or officer of the Company is based in
part on Indemnitee's reliance on such provisions.

         E. In recognition of Indemnitee's need for substantial protection
against personal liability in order to enhance Indemnitee's continued service to
the Company in an effective manner, and Indemnitee's reliance on the aforesaid
provisions of the Constituent Documents, and to provide Indemnitee with express
contractual indemnification (regardless of, among other things, any amendment to
or revocation of such provisions or any change in the composition of the
Company's Board of Directors (the "Board") or any acquisition or business
combination transaction relating to the Company), the Company wishes to provide
in this Agreement for the indemnification of and the advancement of Expenses (as
defined in Section 1(c)) to Indemnitee as set forth in this Agreement and, to
the extent insurance is maintained, for the continued coverage of Indemnitee
under the Company's directors' and officers' liability insurance policies.

         NOW, THEREFORE, the parties hereby agree as follows:

         1. CERTAIN DEFINITIONS. In addition to terms defined elsewhere herein,
the following terms have the following meanings when used in this Agreement with
initial capital letters:

                  (a) "AFFILIATE" has the meaning given to that term in Rule 405
under the Securities Act of 1933, provided, however, that for purposes of this
Agreement the Company and its subsidiaries will not be deemed to constitute
Affiliates of Indemnitee or the Indemnitee.

                  (b) "CLAIM" means any threatened, pending or completed action,
suit or proceeding, or any inquiry or investigation, whether instituted, made or
conducted by the Company or any other party, including without limitation any
governmental entity, that Indemnitee determines might lead to the institution of
any such action, suit or proceeding, whether civil, criminal, administrative,
arbitrative, investigative or other.
<PAGE>   2

                  (c) "EXPENSES" includes attorney's and experts' fees, expenses
and charges and all other costs, expenses and obligations paid or incurred in
connection with investigating, defending, being a witness in or participating in
(including on appeal), or preparing to defend, be a witness in or participate
in, any Claim.

                  (d) "INDEMNIFIABLE LOSSES" means any and all Expenses,
damages, losses, liabilities, judgments, fines, penalties and amounts paid in
settlement (including without limitation all interest, assessments and other
charges paid or payable in connection with or in respect of any of the
foregoing) (collectively, "Losses") relating to, resulting from or arising out
of any act or failure to act by the Indemnitee, or his or her status as any
person referred to in clause (i) of this sentence, (i) in his or her capacity as
a director, officer, employee or agent of the Company, any of its Affiliates or
any other entity as to which the indemnitee is or was serving at the request of
the Company as a director, officer, employee, member, manager, trustee or agent
of another corporation, limited liability company, partnership, joint venture,
trust or other entity or enterprise, whether or not for profit and (ii) in
respect of any business, transaction or other activity of any entity referred to
in clause (i) of this sentence.

         2. BASIC INDEMNIFICATION ARRANGEMENT. The Company will indemnify and
hold harmless Indemnitee, to the fullest extent permitted by the laws of the
State of Delaware in effect on the date hereof or as such laws may from time to
time hereafter be amended to increase the scope of such permitted
indemnification, against all Indemnifiable Losses relating to, resulting from or
arising out of any Claim. The failure by Indemnitee to notify the Company of
such Claim will not relieve the Company from any liability hereunder unless, and
only to the extent that, the Company did not otherwise learn of the Claim and
such failure results in forfeiture by the Company of substantial defenses,
rights or insurance coverage. Except as provided in Section 17, however,
Indemnitee will not be entitled to indemnification pursuant to this Agreement in
connection with any Claim initiated by Indemnitee against the Company or any
director or officer of the Company unless the Company has joined in or consented
to the initiation of such Claim. If so requested by Indemnitee, the Company will
advance within two business days of such request any and all Expenses to
Indemnitee which Indemnitee determines reasonably likely to be payable,
provided, however, that Indemnitee will return, without interest, any such
advance which remains unspent at the final conclusion of the Claim to which the
advance related.

         3. INDEMNIFICATION FOR ADDITIONAL EXPENSES. Without limiting the
generality or effect of the foregoing, the Company will indemnify Indemnitee
against and, if requested by Indemnitee, will within two business days of such
request advance to Indemnitee, any and all attorneys' fees and other Expenses
paid or incurred by Indemnitee in connection with any Claim asserted or brought
by Indemnitee for (i) indemnification or advance payment of Expenses by the
Company under this Agreement or any other agreement or under any provision of
the Company's Constituent Documents now or hereafter in effect relating to
Claims for Indemnifiable Losses and/or (ii) recovery under any directors' and
officers' liability insurance policies maintained by the Company, regardless of
whether Indemnitee ultimately is determined to be entitled to such
indemnification, advance expense payment or insurance recovery, as the case may
be.

         4. PARTIAL INDEMNITY, ETC. If Indemnitee is entitled under any
provision of this Agreement to indemnification by the Company for some or a
portion of any Indemnifiable Loss but not for all of the total amount thereof,
the Company will nevertheless indemnify Indemnitee

<PAGE>   3

for the portion thereof to which Indemnitee is entitled. Moreover,
notwithstanding any other provision of this Agreement, to the extent that
Indemnitee has been successful on the merits or otherwise in defense of any or
all Claims relating in whole or in part to an Indemnifiable Loss or in defense
of any issue or matter therein, including without limitation dismissal without
prejudice, Indemnitee will be indemnified against all Expenses incurred in
connection therewith. In connection with any determination as to whether
Indemnitee is entitled to be indemnified hereunder, there will be a presumption
that Indemnitee is so entitled, which presumption the Company may overcome only
by its adducing clear and convincing evidence to the contrary.

         5. NO OTHER PRESUMPTION. For purposes of this Agreement, the
termination of any Claim by judgment, order, settlement (whether with or without
court approval) or conviction, or upon a plea of nolo contendere or its
equivalent, will not create a presumption that Indemnitee did not meet any
particular standard of conduct or have any particular belief or that a court has
determined that indemnification is not permitted by applicable law.

         6. NON-EXCLUSIVITY, ETC. The rights of Indemnitee hereunder will be in
addition to any other rights Indemnitee may have under the Constituent
Documents, or the substantive laws of the Company's jurisdiction of
incorporation, any other contract or otherwise (collectively, "Other Indemnity
Provisions"); PROVIDED, HOWEVER, that (i) to the extent that Indemnitee
otherwise would have any greater right to indemnification under any Other
Indemnity Provision, Indemnitee will be deemed to have such greater right
hereunder and (ii) to the extent that any change is made to any Other Indemnity
Provision which permits any greater right to indemnification than that provided
under this Agreement as of the date hereof, Indemnitee will be deemed to have
such greater right hereunder. The Company will not adopt any amendment to any of
the Constituent Documents the effect of which would be to deny, diminish or
encumber Indemnitee's right to indemnification under this Agreement or any Other
Indemnity Provision.

         7. LIABILITY INSURANCE AND FUNDING. To the extent the Company maintains
an insurance policy or policies providing directors' and officers' liability
insurance, Indemnitee will be covered by such policy or policies, in accordance
with its or their terms, to the maximum extent of the coverage available for any
director or officer of the Company. The Company may, but will not be required
to, create a trust fund, grant a security interest or use other means, including
without limitation a letter of credit, to ensure the payment of such amounts as
may be necessary to satisfy its obligations to indemnify and advance expenses
pursuant to this Agreement.

         8. SUBROGATION. In the event of payment under this Agreement, the
Company will be subrogated to the extent of such payment to all of the related
rights of recovery of Indemnitee against other persons or entities (other than
Indemnitee's successors). The Indemnitee will execute all papers reasonably
required to evidence such rights (all of Indemnitee's reasonable Expenses,
including attorneys' fees and charges, related thereto to be reimbursed by or,
at the option of Indemnitee, advanced by the Company).

         9. NO DUPLICATION OF PAYMENTS. The Company will not be liable under
this Agreement to make any payment in connection with any Indemnifiable Loss
made against Indemnitee to the extent Indemnitee has otherwise actually received
payment (net of Expenses incurred in connection therewith) under any insurance
policy, the Constituent Documents and Other Indemnity Provisions or otherwise of
the amounts otherwise indemnifiable hereunder.

<PAGE>   4

         10. DEFENSE OF CLAIMS. The Company will be entitled to participate in
the defense of any Claim or to assume the defense thereof, with counsel
reasonably satisfactory to the Indemnitee, PROVIDED that in the event that (i)
the use of counsel chosen by the Company to represent Indemnitee would prevent
such counsel with an actual or potential conflict, (ii) the named parties in any
such Claim (including any impleaded parties) include both the Company and
Indemnitee and Indemnitee shall conclude that there may be one or more legal
defenses available to him or her that are different from or in addition to those
available to the Company, or (iii) any such representation by the Company would
be precluded under the applicable standards of professional conduct then
prevailing, then Indemnitee will be entitled to retain separate counsel (but not
more than one law firm plus, if applicable, local counsel in respect of any
particular Claim) at the Company's expense. The Company will not, without the
prior written consent of the Indemnitee, effect any settlement of any threatened
or pending Claim which the Indemnitee is or could have been a party unless such
settlement solely involves the payment of money and includes an unconditional
release of the Indemnitee from all liability on any claims that are the subject
matter of such Claim.

         11. SUCCESSORS AND BINDING AGREEMENT. (a) The Company will require any
successor (whether direct or indirect, by purchase, merger, consolidation,
reorganization or otherwise) to all or substantially all of the business or
assets of the Company, by agreement in form and substance satisfactory to
Indemnitee and his or her counsel, expressly to assume and agree to perform this
Agreement in the same manner and to the same extent the Company would be
required to perform if no such succession had taken place. This Agreement will
be binding upon and inure to the benefit of the Company and any successor to the
Company, including without limitation any person acquiring directly or
indirectly all or substantially all of the business or assets of the Company
whether by purchase, merger, consolidation, reorganization or otherwise (and
such successor will thereafter be deemed the "Company" for purposes of this
Agreement), but will not otherwise be assignable or delegatable by the Company.

         (b) This Agreement will inure to the benefit of and be enforceable by
the Indemnitee's personal or legal representatives, executors, administrators,
successors, heirs, distributees, legatees and other successors.

         (c) This Agreement is personal in nature and neither of the parties
hereto will, without the consent of the other, assign or delegate this Agreement
or any rights or obligations hereunder except as expressly provided in Sections
11(a) and 11(b). Without limiting the generality or effect of the foregoing,
Indemnitee's right to receive payments hereunder will not be assignable, whether
by pledge, creation of a security interest or otherwise, other than by a
transfer by the Indemnitee's will or by the laws of descent and distribution,
and, in the event of any attempted assignment or transfer contrary to this
Section 11(c), the Company will have no liability to pay any amount so attempted
to be assigned or transferred.

         12. NOTICES. For all purposes of this Agreement, all communications,
including without limitation notices, consents, requests or approvals, required
or permitted to be given hereunder will be in writing and will be deemed to have
been duly given when hand delivered or dispatched by electronic facsimile
transmission (with receipt thereof orally confirmed), or five business days
after having been mailed by United States registered or certified mail, return
receipt requested, postage prepaid or one business day after having been sent
for next-day delivery by a nationally recognized overnight courier service,
addressed to the Company (to the attention of the Secretary

<PAGE>   5

of the Company) and to the Indemnitee at the addresses shown on the signature
page hereto, or to such other address as any party may have furnished to the
other in writing and in accordance herewith, except that notices of changes of
address will be effective only upon receipt.

         13. GOVERNING LAW. The validity, interpretation, construction and
performance of this Agreement will be governed by and construed in accordance
with the substantive laws of the State of Delaware, without giving effect to the
principles of conflict of laws of such State. Each party consents to
non-exclusive jurisdiction of any Delaware state or federal court or any court
in any other jurisdiction in which a Claim is commenced by a third person for
purposes of any action, suit or proceeding hereunder, waives any objection to
venue therein or any defense based on forum non conveniens or similar theories
and agrees that service of process may be effected in any such action, suit or
proceeding by notice given in accordance with Section 12.

         14. VALIDITY. If any provision of this Agreement or the application of
any provision hereof to any person or circumstance is held invalid,
unenforceable or otherwise illegal, the remainder of this Agreement and the
application of such provision to any other person or circumstance will not be
affected, and the provision so held to be invalid, unenforceable or otherwise
illegal will be reformed to the extent, and only to the extent, necessary to
make it enforceable, valid or legal.

         15. MISCELLANEOUS. No provision of this Agreement may be waived,
modified or discharged unless such waiver, modification or discharge is agreed
to in writing signed by Indemnitee and the Company. No waiver by either party
hereto at any time of any breach by the other party hereto or compliance with
any condition or provision of this Agreement to be performed by such other party
will be deemed a waiver of similar or dissimilar provisions or conditions at the
same or at any prior or subsequent time. No agreements or representations, oral
or otherwise, expressed or implied with respect to the subject matter hereof
have been made by either party that are not set forth expressly in this
Agreement. References to Sections are to references to Sections of this
Agreement.

         16. COUNTERPARTS. This Agreement may be executed in one or more
counterparts, each of which will be deemed to be an original but all of which
together will constitute one and the same agreement.

         17. LEGAL FEES AND EXPENSES. It is the intent of the Company that the
Indemnitee not be required to incur legal fees and or other Expenses associated
with the interpretation, enforcement or defense of Indemnitee's rights under
this Agreement by litigation or otherwise because the cost and expense thereof
would substantially detract from the benefits intended to be extended to the
Indemnitee hereunder. Accordingly, without limiting the generality or effect of
any other provision hereof, if it should appear to the Indemnitee that the
Company has failed to comply with any of its obligations under this Agreement or
in the event that the Company or any other person takes or threatens to take any
action to declare this Agreement void or unenforceable, or institutes any
litigation or other action or proceeding designed to deny, or to recover from,
the Indemnitee the benefits provided or intended to be provided to the
Indemnitee hereunder, the Company irrevocably authorizes the Indemnitee from
time to time to retain counsel of Indemnitee's choice, at the expense of the
Company as hereafter provided, to advise and represent the Indemnitee in
connection with any such interpretation, enforcement or defense, including
without limitation the initiation or defense of any litigation or other legal
action,

<PAGE>   6

whether by or against the Company or any director, officer, stockholder or other
person affiliated with the Company, in any jurisdiction. Notwithstanding any
existing or prior attorney-client relationship between the Company and such
counsel, the Company irrevocably consents to the Indemnitee's entering into an
attorney-client relationship with such counsel, and in that connection the
Company and the Indemnitee agree that a confidential relationship shall exist
between the Indemnitee and such counsel. Without respect to whether the
Indemnitee prevails, in whole or in part, in connection with any of the
foregoing, the Company will pay and be solely financially responsible for any
and all attorneys' and related fees and expenses incurred by the Indemnitee in
connection with any of the foregoing.

         18. CERTAIN INTERPRETIVE MATTERS. No provision of this Agreement will
be interpreted in favor of, or against, either of the parties hereto by reason
of the extent to which any such party or its counsel participated in the
drafting thereof or by reason of the extent to which any such provision is
inconsistent with any prior draft hereof or thereof.

<PAGE>   7

         IN WITNESS WHEREOF, Indemnitee has executed and the Company has caused
its duly authorized representative to execute this Agreement as of the date
first above written.

                                      NETGENICS, INC.
                                      1700 East Ninth Street, Suite 1600
                                      Cleveland, Ohio 44114

                                      By:
                                             -----------------------------------
                                             Name:
                                             Title:

                                      [INDEMNITEE]
                                      [Address]

                                             -----------------------------------
                                                        [Indemnitee]

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