<PAGE>
 
                      SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C. 20549

                                   FORM 10-Q

(Mark One)
     [X]  QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE 
          SECURITIES EXCHANGE ACT OF 1934
 
For the quarterly period ended March 31, 1998

                                      or

     [_]  TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE 
          SECURITIES EXCHANGE ACT OF 1934

                       Commission File Number:  0-27188
                                                -------

                              PHARMACOPEIA, INC.
 
--------------------------------------------------------------------------------
            (Exact name of registrant as specified in its charter)
 
Delaware                                                33-0557266
--------------------------------------------------------------------------------
(State or other jurisdiction of             (I.R.S. Employer Identification No.)
incorporation or organization)
 
101 College Road East, Princeton, New  Jersey                         08540
--------------------------------------------------------------------------------
(Address of principal executive offices)                           (Zip code)

                                (609) 452-3600
--------------------------------------------------------------------------------
             (Registrant's telephone number, including area code)

                                   Not Applicable
--------------------------------------------------------------------------------
  (Former name, former address and former fiscal year, if changed since last 
                                    report)

Indicate by check mark whether the registrant (1) has filed all reports required
to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during
the preceding 12 months (or such shorter period that the registrant was required
to file such reports) and (2) has been subject to such filing requirements for
the past 90 days -- Yes  X     No   
                       -----     _____

Indicate the number of shares outstanding of each of the issuer's classes of
common stock, as of the latest practicable date:

                  CLASS                         OUTSTANDING AT APRIL 13, 1998
     -------------------------------         ----------------------------------
     Common Stock, $.0001 par value                     11,811,079
<PAGE>
 
                              PHARMACOPEIA, INC.

                                   FORM 10-Q

                               TABLE OF CONTENTS

<TABLE>
<CAPTION>
ITEM                                                                                            Page
----                                                                                            ----
<S>                                                                                           <C> 
PART I.  FINANCIAL INFORMATION
 
Item 1.   Financial Statements:
 
          Consolidated Balance Sheets-March 31, 1998 and December 31, 1997                      3
 
          Consolidated Statements of Operations-Three Months Ended                              4
          March 31, 1998 and 1997
 
          Consolidated Statements of Cash Flows-Three Months Ended                              5
          March 31, 1998 and 1997

          Notes to Consolidated Financial Statements                                           6-7

Item 2.   Management's Discussion and Analysis of Financial Condition and                      7-10
          Results of Operations

PART II.  OTHER INFORMATION
 
Item 6.   Exhibits and Reports on Form 8-K                                                    11-13
 
SIGNATURE                                                                                       14
INDEX TO EXHIBITS                                                                               15
</TABLE>

                                      -2-
<PAGE>
 
                                    PART I
                             FINANCIAL INFORMATION

ITEM 1.  FINANCIAL STATEMENTS
                       PHARMACOPEIA, INC. AND SUBSIDIARY
                          CONSOLIDATED BALANCE SHEETS
                   (DOLLARS IN THOUSANDS, EXCEPT SHARE DATA)

<TABLE>
<CAPTION>
                                                                           MARCH 31,     December 31, 
                                                                             1998           1997
                                                                          ----------------------------
                                                                          (Unaudited)
ASSETS
<S>                                                                       <C>                 <C>   
Current assets:
 Cash and cash equivalents                                                $  3,492            $   9,590
 Marketable securities                                                      64,244               60,166
 Prepaid expenses and other current assets                                   2,458                1,890
                                                                          -----------------------------
Total current assets                                                        70,194               71,646
                                                                          -----------------------------
 
Non-current investments in marketable securities                             8,719               12,865
Property and equipment, net                                                 10,528               10,874
Other assets                                                                   329                  302
                                                                          -----------------------------
                                                                          $ 89,770            $  95,687
                                                                          =============================
LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
 Accounts payable                                                         $     993            $  1,756
 Accrued liabilities                                                          1,818               2,726
 Notes payable, current portion                                                 680                 690
 Deferred revenue                                                            15,322              16,091
                                                                          -----------------------------
Total current liabilities                                                    18,813              21,263
 
Notes payable, long-term portion                                                558                 712
Deferred revenue, long-term                                                   1,993               3,275
 
Commitments
 
Stockholders' equity:
 Preferred stock, $.0001 par value; 2,000,000 shares
  authorized; none issued and outstanding
 Common stock, $.0001 par value; 40,000,000 shares authorized;
  11,811,079 and 11,270,953 shares issued and outstanding at
  March 31, 1998 and December 31, 1997, respectively                              1                   1
  Additional paid-in capital                                                105,103             104,909
 Accumulated deficit                                                        (36,698)            (34,473)
                                                                          -----------------------------
Total stockholders' equity                                                   68,406              70,437
                                                                          -----------------------------
                                                                          $  89,770            $ 95,687
                                                                          =============================
</TABLE> 

 See accompanying notes to these unaudited consolidated financial statements.

                                      -3-
<PAGE>
 
                       PHARMACOPEIA, INC. AND SUBSIDIARY

                     CONSOLIDATED STATEMENTS OF OPERATIONS
                 (DOLLARS IN THOUSANDS, EXCEPT PER SHARE DATA)

<TABLE>
<CAPTION>
                                                            THREE MONTHS ENDED MARCH 31,
                                                                 1998          1997
                                                            ----------------------------
                                                                     (UNAUDITED)
<S>                                                         <C>             <C>   
Contract revenue                                            $     6,432     $     5,932
 
Operating expenses:
 Research and development:
  Collaborative                                                   4,420           4,151
  Proprietary                                                     3,724           2,729
 General and administrative                                       1,587           1,458
                                                            ----------------------------
Operating loss                                                   (3,299)         (2,406)
 
Interest income                                                   1,116           1,064
Interest expense                                                    (43)            (67)
                                                            ----------------------------
Net loss                                                    $    (2,226)    $    (1,409)
                                                            ============================
Basic net loss per share                                    $      (.19)    $      (.13)
                                                            ============================
 
Weighted-average number of common shares
 outstanding during the period                               11,798,024      11,269,752
                                                            ============================
</TABLE>


 See accompanying notes to these unaudited consolidated financial statements.

                                      -4-
<PAGE>
 
                       PHARMACOPEIA, INC. AND SUBSIDIARY

                     CONSOLIDATED STATEMENTS OF CASH FLOWS
                            (DOLLARS IN THOUSANDS)

<TABLE>
<CAPTION>
                                                                           THREE MONTHS ENDED MARCH 31,
                                                                                1998           1997
                                                                           ----------------------------
                                                                                    (UNAUDITED)
CASH FLOWS FROM OPERATING ACTIVITIES
<S>                                                                        <C>            <C> 
Net loss                                                                   $    (2,226)   $    (1,409)
Adjustments to reconcile net loss to net cash provided
  by (used in) operating activities:
  Depreciation                                                                     835            619
  Amortization                                                                       1             10
  Changes in operating assets and liabilities:
  (Increase) in prepaid expenses and other current assets                         (568)          (670)
  (Increase) decrease in other assets                                              (27)            88
  (Decrease) in accounts payable                                                  (763)           (35)
  (Decrease) in accrued liabilities                                               (908)          (160)
  Increase (decrease) in deferred revenue                                       (2,051)            95
                                                                           ----------------------------
Net cash (used in) operating activities                                         (5,707)        (1,462)
 
CASH FLOWS FROM INVESTING ACTIVITIES
Capital expenditures                                                              (489)        (1,098)
Purchase of marketable securities                                              (19,254)       (28,101)
Proceeds from maturities of marketable securities                               19,322         19,182
                                                                           ----------------------------
Net cash used in investing activities                                             (421)       (10,017)
 
CASH FLOWS FROM FINANCING ACTIVITIES
Net proceeds from issuance of common stock                                         194              7
Repayments of notes payable                                                       (164)          (173)
                                                                           ----------------------------  
Net cash provided by (used in) financing activities                                 30           (166)
                                                                           ----------------------------
 
Decrease in cash and cash equivalents                                           (6,098)       (11,645)
Cash and cash equivalents at beginning of period                                 9,590         17,059
                                                                           ----------------------------
Cash and cash equivalents at end of period                                 $     3,492    $     5,414
                                                                           ============================
</TABLE>

 See accompanying notes to these unaudited consolidated financial statements.

                                      -5-
<PAGE>
 
                       PHARMACOPEIA, INC. AND SUBSIDIARY

                  Notes to Consolidated Financial Statements
                                  (UNAUDITED)

NOTE (1) -- BASIS OF PRESENTATION

     The unaudited consolidated financial statements have been prepared in
accordance with generally accepted accounting principles for interim financial
information.  Accordingly, they do not include all of the information and
footnotes required by generally accepted accounting principles for complete
financial statements. In the opinion of management, all adjustments (consisting
of normal recurring accruals) considered necessary for a fair presentation have
been included. The Company's wholly-owned subsidiary, Micro Acquisition
Corporation, was incorporated in the state of Delaware on January 9, 1998. All
intercompany balances have been eliminated in consolidation. Interim results are
not necessarily indicative of the results that may be expected for the year.
For further information, refer to the financial statements and footnotes thereto
included in the Company's Annual Report on Form 10-K, as amended, for the year
ended December 31, 1997.

NOTE (2) -- BASIC NET LOSS PER SHARE

     Basic net loss per share is based on net loss for the relevant period
divided by the weighted average number of common shares issued and outstanding
during the period. Common Stock equivalents such as stock options and warrants
are not included as their effect is anti-dilutive.

NOTE (3) -- IMPACT OF RECENTLY ISSUED ACCOUNTING STANDARDS

     On January 1, 1998 the Company adopted SFAS No. 130, "Reporting
Comprehensive Income" ("SFAS No. 130"). SFAS No. 130 establishes standards for
the reporting and display of comprehensive income and its components and is
applied to all enterprises. The adoption of SFAS No. 130 had no impact on the
Company's consolidated results of operations, financial position or cash flows.

     In June 1997, the Financial Accounting Standards Board issued SFAS No. 131,
"Disclosures about Segments of an Enterprise and Related Information" ("SFAS No.
131").  SFAS No. 131 establishes standards for the way that public business
enterprises report information about operating segments in annual financial
statements and requires that those enterprises report selected information about
operating segments in interim financial reports issued to stockholders.  It also
establishes standards for related disclosures about products and services,
geographic areas, and major customers.  SFAS No. 131 is effective for financial
statements for fiscal years beginning after December 15, 1997.  The Company will
adopt the new requirements in conjunction with its 1998 Form 10-K.  The adoption
of SFAS No. 131 will have no significant impact on the Company's financial
reporting, except with respect to reporting information regarding Molecular 
Simulations Incorporated in the event that the transaction described under 
"Proposed Merger" below is consummated.

     On February 4, 1998, the Company and Molecular Simulations Incorporated
("MSI") announced the execution of a definitive merger agreement under which the
Company will acquire MSI in a tax-free, stock-for-stock transaction to be
accounted for on a pooling of interests basis. The Company will acquire all of
the outstanding stock of MSI and will assume the outstanding MSI options, which
will then be exercisable for shares of the Company's Common Stock. The Company
anticipates finalizing the merger transaction during the second quarter of 1998
once shareholder approval has been received. MSI is a provider of molecular
modeling and simulation software. MSI designs, develops, markets and supports
software that facilitates the discovery and development of new products and
processes in the pharmaceutical, biotechnology, chemical, petrochemical and
materials industries. As of December 31, 1997 MSI had total assets of $46,500
and for the year ended December 31, 1997 MSI had total revenue of $56,700 and
net income of $5,400.

                                      -6-
<PAGE>
 
ITEM 2. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND 
        RESULTS OF OPERATIONS

OVERVIEW

        The following Management's Discussion and Analysis is based on
historical financial results of Pharmacopeia, Inc. and Subsidiary
("Pharmacopeia" or the "Company") and includes certain forward-looking
statements that do not specifically reflect the impact that the proposed merger
described below under the caption "Proposed Merger" may have on future financial
performance of the post-merger company. Such performance cannot be predicted and
may not follow the same historical trends as those presented in the following
discussion.

        Pharmacopeia was incorporated in March 1993 and is engaged in research
and development and chemical library production for collaborations and for its
own use. The Company's research and development has focused on efficient, cost
effective, high throughput systems for synthesizing and screening large
libraries of chemicals for new drug discovery and optimization. The Company has
incurred losses since inception and, as of March 31, 1998 had an accumulated
deficit of $36.7 million. The Company anticipates incurring additional losses
over at least the next several years as it expands its research and development
and chemical library production efforts. The Company expects that its losses
will fluctuate from quarter to quarter and that such variations may be
substantial.

RESULTS OF OPERATIONS

        The Company expects that its revenue sources for at least the next
several years will be limited to future drug discovery collaboration payments
from Schering Corporation and Schering-Plough Ltd., Berlex Laboratories, Inc.,
Novartis Corporation, Bayer Corporation, Daiichi Pharmaceuticals Co., Ltd., N.V.
Organon, Zeneca Pharmaceuticals and Bristol-Myers Squibb and from other
customers under existing arrangements and others that may be entered into in the
future. The timing and amounts of such revenues, if any, will likely fluctuate.
Historical results should not be viewed as indicative of future operating
results. The Company will be required to conduct significant research,
development and production activities during the next several years to fulfill
its obligations under its drug discovery collaborative agreements and to develop
other collaborations and technologies. The Company does not anticipate having
net income in the next several years.

THREE MONTHS ENDED MARCH 31, 1998 AND 1997

        Revenues totaled $6.4 million and $5.9 million in the three months ended
March 31, 1998 and 1997. The increase of $.5 million in revenues is primarily
the result of the Company's expanded efforts in the library outlicensing
collaborations with Novartis and Bayer.

        The Company incurred research and development expenses of $8.1 million
and $6.9 million in the three months ended March 31, 1998 and 1997,
respectively. The $1.2 million increase primarily reflects a 36% increase in
proprietary research and development as Pharmacopeia continues to invest in
internal discovery programs, ultra high-throughput

                                      -7-
<PAGE>
 
screening, and informatics. Research and development expenses are expected to
continue to increase as the Company further expands its activities and incurs,
among other things, expenses related to additional staff increases, increased
rent for expanded facilities, and increased equipment and reagent purchases.
 
     General and administrative expenses were $1.6 million and $1.5 million in
the three months ended March 31, 1998 and 1997, respectively. The increase is
primarily attributable to increased payroll and personnel expenses as the
Company continued to hire additional management and administrative personnel.

     The Company had interest income of $1.1 million in both the three months
ended March 31, 1998 and March 31, 1997 as a result of the average balance of
cash, cash equivalents and marketable securities remaining constant for both
periods. Interest expense for both periods is a result of interest incurred on
notes payable.

LIQUIDITY AND CAPITAL RESOURCES

     As of March 31, 1998, the Company had working capital of $51.4 million.
The Company has funded its activities through March 31, 1998 primarily through
the sale of equity securities and funding under collaborative arrangements.
From inception through March 31, 1998, the Company received $105.1 million in
net proceeds from equity financing and received $64.3 million in research and
development, license fees and milestone payments under collaborative agreements.

     The Company's funds are currently invested in U.S. Treasury and government
agency obligations, investment grade commercial paper and other short-term money
market instruments. The Company may also invest such proceeds in investment
grade, interest-bearing securities having a maximum maturity of two years. As of
March 31, 1998, the Company's cash and cash equivalents totaled $3.5 million. In
addition, the Company had marketable securities of $72.9 million.

     In connection with the Company's agreement with the Trustees of Columbia
University and Cold Spring Harbor Laboratory, the Company is required to pay
annual license fees. The Company is also required to pay to Columbia University
certain royalties.

     In addition, as of March 31, 1998, the Company had outstanding commitments
for construction and equipment purchases totaling $.2 million. The Company
anticipates that its capital requirements will continue at approximately the
same level over the next two years as the Company expands its research and
development activities. In connection with such expansion, the Company expects
to incur substantial expenditures for hiring additional management and
scientific and administrative personnel, and for planned expansion and upgrading
of its facilities, including acquisition of additional equipment.

     The Company anticipates that its existing capital resources will be
adequate to fund the Company's operations at least through 1999.  There can be
no assurance that changes will not occur that would consume available capital
resources before such time.  The Company's capital 

                                      -8-
<PAGE>
 
requirements depend on numerous factors, including the ability of the Company to
extend existing collaborations and enter into additional collaborative
arrangements, competing technological and market developments, changes in the
Company's existing collaborative relationships, the cost of filing, prosecuting,
defending and enforcing patent claims and other intellectual property rights and
the outcome of related litigation, the purchase of additional capital equipment,
acquisitions of other businesses or technologies, the progress of the Company's
drug discovery programs and the progress of the Company's customers' milestone
and royalty producing activities. There can be no assurance that additional
funding, if necessary, will be available on favorable terms, if at all. The
Company's forecasts of the period of time through which its financial resources
will be adequate to support its operations is forward looking information, and
actual results could vary. The factors described earlier in this paragraph will
impact the Company's future capital requirements and the adequacy of its
available funds.

PROPOSED MERGER

     On February 4, 1998, Pharmacopeia, Micro Acquisition Corporation, a wholly-
owned subsidiary of Pharmacopeia ("MAC") and Molecular Simulations Incorporated
("MSI") executed a definitive merger agreement (the "Merger Agreement") pursuant
to which Pharmacopeia will acquire MSI in a tax-free, stock-for-stock
transaction, which Pharmacopeia expects will qualify for accounting treatment on
a "pooling-of-interests" basis.

     Pursuant to the Merger Agreement, MAC will be merged into MSI with MSI as
the surviving corporation. Assuming that outstanding options to purchase shares
of common stock of MSI are not exercised before the effective time of the
merger, Pharmacopeia will (a) acquire all of the outstanding capital stock of
MSI in exchange for approximately 7.1 million newly-issued shares of
Pharmacopeia Common Stock and (b) assume the outstanding MSI options, which will
then be exercisable for shares of Pharmacopeia Common Stock, potentially
resulting in the issuance of up to an additional 1.6 million newly-issued shares
of Pharmacopeia Common Stock.

     The transaction is subject to certain conditions, including stockholder
approvals, the effectiveness of a registration statement under the federal
securities laws relating to the Pharmacopeia Common Stock to be issued in the
merger, the listing of such Pharmacopeia Common Stock on the Nasdaq National
Market and the expiration of applicable waiting periods under pre-merger
notification regulations. Pharmacopeia and an affiliate of MSI have received
notices of the grant of early termination of such waiting periods.  On May 8,
1998 Pharmacopeia's registration statement under the federal securities laws
relating to the Pharmacopeia Common Stock to be issued in the merger was
declared effective.

     As of December 31, 1997 MSI had total assets of $46.5 million and for the
year ended December 31, 1997 MSI had total revenue of $56.7 million and net
income of $5.4 million.

     After the closing of the merger, Pharmacopeia will file, as part of a
current Report on Form 8-K, unaudited pro forma combined condensed financial
statements that give effect to the merger.

                                      -9-
<PAGE>
 
                                    PART II

                               OTHER INFORMATION

ITEM 6.  EXHIBITS AND REPORTS ON FORM 8-K

(a)  Exhibits:

<TABLE>
<C>                 <S>
3.1******           Restated Certificate of Incorporation of the Registrant.
3.3******           Bylaws of the Registrant, as amended.
3.3(a)********      Amendment to Bylaws of Pharmacopeia dated July 31, 1997.
4.3*                Stockholders Rights Agreement, dated February 15, 1995.
10.1*               Series A and Series B Preferred Stock Purchase Agreement, dated July 21, 1993.
10.2*               Series B Preferred Stock Purchase Agreement, dated March 11, 1994.
10.3*               Series C Preferred Stock Purchase Agreement, dated December 22, 1994.
10.4*               Series D Preferred Stock Purchase Agreement, dated February 15, 1995.
10.5**#             Amended 1994 Incentive Stock Plan.
10.5(a)*******#     Amendment No. 3 to the 1994 Incentive Stock Plan dated May 9, 1997.
10.6*#              1995 Employee Stock Purchase Plan.
10.7*#              1995 Director Option Plan.
10.8*+              Library Collection Agreement, dated as of October 1, 1995, between Pharmacopeia and
                    Novartis Corporation.
10.9*+              Research, License, and Royalty Agreement, dated as of February 15, 1995, between
                    Pharmacopeia and Berlex Laboratories, Inc.
10.9(a)*******+     Amendment No. 1 to Research, License and Royalty Agreement between the Company and
                    Berlex Laboratories, Inc. dated November 27, 1996.
10.9(b)*******+     Amendment No. 2 to Research, License and Royalty Agreement between the Company and
                    Berlex Laboratories, Inc. dated June 30, 1997.
10.9(c)*********+   Amendment No.3 to Research, License and Royalty Agreement between the Company and
                    Berlex Laboratories, Inc. dated November 21, 1997.
10.10*+             License Agreement, dated as of October 6, 1995, among Pharmacopeia, the Trustees of
                    Columbia University in the City of New York and Cold Spring Harbor Laboratory.
10.11*+             Collaboration Agreement, dated as of December 22, 1994, between Pharmacopeia and
                    Schering Corporation and Schering-Plough, Ltd.
10.11(b)*******+    Amendment No. 2 to Collaboration Agreement and Random Library Agreement between the
                    Company and Schering Corporation and Schering-Plough, Ltd. dated as of April 22, 1996.
10.11(c)*******+    Amendment No. 3 to Collaboration Agreement and Random Library Agreement between the
                    Company and Schering Corporation and Schering-Plough, Ltd. dated as of April 21, 1997.
10.12*+             Random Library Agreement, dated as of December 22, 1994, between Pharmacopeia and
                    Schering Corporation and Schering-Plough, Ltd.
10.13*              Lease Agreement between Pharmacopeia and Eastpark at 8A.
10.13(a)**          Amendment dated as of January 22, 1996 to Lease Agreement between Pharmacopeia and
                    Eastpark at 8A.
</TABLE> 

                                      -10-
<PAGE>
 
<TABLE> 
<S>                 <C> 
10.13(b)****        Third Amendment to Lease Agreement dated March 31, 1996 between Pharmacopeia and
                    Eastpark at 8A.
10.14*              Sublease, dated as of December 7, 1994, between Pharmacopeia and Enichem Americas, Inc.
10.15*              Lease, dated as of May 2, 1994, between Pharmacopeia and College Road Associates
                    Limited, as amended.
10.15(a)**          Lease dated as of December 1, 1995 between Pharmacopeia and College Road Associates, as
                    amended.
10.15(b)****        Third Execution and Modification of lease dated June 7, 1996, between Pharmacopeia and
                    College Road Associates Limited.
10.17*#             Employment Agreement, dated October 4, 1994, between the Company and Lewis J. Shuster.
10.18*********#     Employment Agreement effective November 1, 1997 between the Company and Joseph A.
                    Mollica, Ph.D.
10.20*#             Employment Agreement, dated June 3, 1993, between the Company and John J. Baldwin, Ph.D.
10.21*#             Employment Agreement, dated December 2, 1993, between the Company and Nolan H.
                    Sigal, M.D., Ph.D.
10.22*#             Consulting Agreement, dated April 30, 1993, between the Company and W. Clark Still,
                    Ph.D.
10.23*              Warrant to purchase Common Stock issued to Columbia University.
10.24*              Warrant to purchase Common Stock issued to Cold Spring Harbor Laboratory.
10.25**+            Collaboration Agreement effective as of December 31, 1995 between Pharmacopeia and
                    Bayer.
10.26**+            Random Library Agreement effective as of December 31, 1995 between Pharmacopeia and
                    Bayer.
10.30***+           Collaborative Agreement dated as of March 29, 1996 with Daiichi Pharmaceutical Co., Ltd.
10.30(a)*******+    Amendment No. 1 to Collaboration Agreement between the  Company and Daiichi
                    Pharmaceutical Co., Ltd. dated April 14, 1997.
10.31****+          Research Agreement, between Pharmacopeia, Inc. and N.V. Organon dated May 31, 1996.
10.32*****#         Employment Agreement, dated June 20, 1996, between the Company and Stephen A. Spearman,
                    Ph.D.
10.33*****          Lease Agreement, dated June 21, 1996, between Pharmacopeia and South Brunswick Rental
                    I, Ltd.
10.34**********+    Collaboration and License Agreement between Pharmacopeia, Inc. and Bristol-Myers Squibb
                    Company dated November 26, 1997.
11.1*               Statement re Computation of Per Share Earnings.
27.1                Financial Data Schedule
</TABLE>

_________________
* Incorporated by reference to the same numbered exhibit filed with the
Company's Registration Statement on Form S-1 No. 33-93460.
** Incorporated by reference to the same numbered exhibit filed with the
Company's Form 10-K for the year ended December 31, 1995.

                                      -11-
<PAGE>
 
*** Incorporated by reference to the same numbered exhibit filed with the
Company's Form 10-Q for the quarter ended March 31, 1996.
**** Incorporated by reference to the same numbered exhibit filed with the
Company's Form 10-Q for the quarter ended June 30, 1996.
***** Incorporated by reference to the same numbered exhibit filed with the
Company's Form 10-Q for the quarter ended September 30, 1996.
****** Incorporated by reference to the same numbered exhibit filed with the
Company's Form 10-K for the year ended December 31, 1996.
******* Incorporated by reference to the same numbered exhibit filed with the
Company's Form 10-Q for the quarter ended June 30, 1997.
******** Incorporated by reference to the same numbered exhibit filed with the
Company's form 10-Q for the quarter ended September 30, 1997.
********* Incorporated by reference to the same numbered exhibit filed with the
Company's Form 10-K for the year ended December 31, 1997.
********** Incorporated by reference to the same numbered exhibit filed with the
Company's Form 10-K/ 
A-2 for the year ended December 31, 1997
+  Confidential treatment granted.
#  Represents a management contract or compensatory plan or arrangement.


(b)  REPORTS ON FORM 8-K

     (i)  Current report on Form 8-K dated February 4, 1998 (filed February 5,
1998) reported under Item 2 the Agreement and Plan of Merger and Reorganization
among Pharmacopeia, Inc., Micro Acquisition Corporation and Molecular
Simulations Incorporated and reported under Item 7 the list of related exhibits.

                                      -12-
<PAGE>
 
                                  SIGNATURES


     Pursuant to the requirements of the Securities Exchange Act of 1934, the
Registrant has duly caused this report to be signed on its behalf by the
undersigned, thereunto duly authorized.


                                   PHARMACOPEIA, INC.


                                   By: /s/ LEWIS J. SHUSTER
                                       ---------------------------------------
                                       Lewis J. Shuster
                                       Executive Vice President, Corporate
                                       Development & Chief Financial Officer
                                       (Duly Authorized Officer and Chief
                                        Accounting Officer)

                                   Date:  May 14, 1998

                                      -13-
<PAGE>
 
                              PHARMACOPEIA, INC.
                               INDEX TO EXHIBITS

<TABLE>
<CAPTION>
EXHIBIT NUMBER      EXHIBIT NAME                            PAGE
<S>                 <C>                                     <C> 
27.1                Financial Data Schedule
</TABLE>

                                      -14-