<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 September 30, 1998

                                      or

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

                       Commission File Number:  0-27118
                                                -------

                              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)

CN 5350, Princeton, New Jersey                                     08543-5350
--------------------------------------------------------------------------------
(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:

<TABLE>
<CAPTION>
               Class                        Outstanding at September 30, 1998
  ----------------------------------      -------------------------------------
<S>                                                 <C>
    Common Stock, $.0001 par value                      19,004,735
</TABLE>
<PAGE>
 
                       PHARMACOPEIA, INC. AND SUBSIDIARY
                                        
                                   Form 10-Q

                               Table of Contents

<TABLE>
<CAPTION>

  ITEM                                                                                           PAGE
  ----                                                                                           ----
 
PART I.  FINANCIAL INFORMATION
 
Item 1.      Financial Statements:
<S>                                                                                       <C>
             Consolidated Balance Sheets-September 30, 1998 and December 31, 1997                 3
                                                                                                  
             Consolidated Statements of Operations-Three and Nine Months Ended
              September 30, 1998 and 1997                                                         4

             Consolidated Statements of Cash Flows-Nine Months Ended
              September 30, 1998 and 1997                                                         5

             Notes to Consolidated Financial Statements                                          6-8
                                                                                               
Item 2.      Management's Discussion and Analysis of Financial Condition and
              Results of Operations                                                              8-10
 
PART II. OTHER INFORMATION
 
Item 6.      Exhibits and Reports on Form 8-K
                                                                                                11-14
SIGNATURE
                                                                                                  15
INDEX TO EXHIBITS
                                                                                                  16
</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>
                                                                        SEPTEMBER 30,        DECEMBER 31, 
                                                                            1998                 1997
                                                                    -----------------------------------------
                                                                         (Unaudited)
<S>                                                                   <C>                  <C>
ASSETS
Current assets:
  Cash and cash equivalents                                                   $   37,562           $   24,609
  Marketable securities                                                           45,662               60,166
  Trade receivables, net of allowance for doubtful accounts of $505
   and $466, respectively                                                         13,159               19,424
  Prepaid expenses and other current assets                                        5,289                4,671
                                                                    -----------------------------------------    
     Total current assets                                                        101,672              108,870
                                                                    -----------------------------------------
 
  Non-current investments in marketable securities                                                     12,865
  Property and equipment, net                                                     13,142               13,141
  Software development costs, net                                                  3,417                3,437
  Investment in joint venture                                                                           1,013
  Other assets                                                                     1,583                  725
                                                                    -----------------------------------------    
                                                                              $  119,814           $  140,051
                                                                    =========================================
                                                                                       
LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
  Accounts payable                                                            $    3,593           $    4,232
  Accrued liabilities                                                             16,898               18,294
  Notes payable, current portion                                                   1,268                1,390
  Deferred revenue, current portion                                               24,200               29,345
                                                                    -----------------------------------------
 
     Total current liabilities                                                    45,959               53,261
                                                                    -----------------------------------------
 
  Notes payable, long-term portion                                                   458                1,412
  Other long-term liabilities                                                        119                  440
  Deferred revenue, long term                                                      1,631                4,342
  Minority interest in joint venture                                               1,065
 
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;
   19,004,735 and 18,804,524 shares issued and outstanding at
   September 30, 1998 and December 31, 1997, respectively                              1                    1
  Additional paid in capital                                                     145,304              144,440
  Accumulated deficit                                                            (74,037)             (62,657)
  Cumulative translation adjustment                                                 (686)              (1,188)
                                                                    -----------------------------------------
     Total stockholders' equity                                                   70,582               80,596
                                                                    -----------------------------------------
                                                                              $  119,814           $  140,051
                                                                    =========================================
</TABLE>

        See accompanying notes to these unaudited financial statements.

                                      -3-
<PAGE>
 
                       PHARMACOPEIA, INC. AND SUBSIDIARY
                     CONSOLIDATED STATEMENTS OF OPERATIONS
                 (DOLLARS IN THOUSANDS, EXCEPT PER SHARE DATA)

                                        
<TABLE>
<CAPTION>
                                                 THREE MONTHS ENDED SEPTEMBER 30,           NINE MONTHS ENDED SEPTEMBER 30,
                                                     1998                1997                   1998              1997
                                             ----------------------------------------     ----------------------------------
                                                             (UNAUDITED)                               (UNAUDITED)
 
 
Revenue:
<S>                                            <C>                     <C>                  <C>              <C>
       Contract                                              $ 6,971          $ 5,234             $ 20,426           $16,752
       Software license, service and other                    12,309           10,846               36,822            33,104
       Hardware                                                1,791            1,985                4,671             5,086
                                             ----------------------------------------     ----------------------------------
                  Total revenue                               21,071           18,065               61,919            54,942
 
Cost and expenses:
       Software, license and other                               719              782                2,282             2,337
       Hardware                                                1,565            1,793                3,985             4,498
       Research and development:
              Collaborative                                    5,462            3,968               14,597            12,297
              Proprietary                                      6,722            6,358               20,687            18,325
       Sales, general and administrative                       9,188            7,444               26,078            21,812
       Merger related costs                                        0                0                7,998                 0
                                             ----------------------------------------     ----------------------------------
                 Total costs and expenses                     23,656           20,345               75,627            59,269
                                             ----------------------------------------     ----------------------------------
Operating loss                                                (2,585)          (2,280)             (13,708)           (4,327)
Interest and other income, net                                 1,052            1,303                3,001             3,554
                                             ----------------------------------------     ----------------------------------
Loss before provision for income taxes                        (1,533)            (977)             (10,707)             (773)
Provision for income taxes                                       550              547                  542             1,795
                                             ----------------------------------------     ----------------------------------
Net loss                                                     $(2,083)         $(1,524)            $(11,249)          $(2,568)
                                             ========================================     ==================================
 
Basic net loss per share                                      $(0.11)          $(0.08)              $(0.60)           $(0.14)
                                             ========================================     ==================================
Diluted net loss per share                                    $(0.11)          $(0.08)              $(0.60)           $(0.14)
                                             ========================================     ==================================
Weighted average shares of common stock,
  outstanding-basic                                           18,968           18,562               18,905            18,396
Weighted average shares of common stock, and
  common stock equivalents                                    18,968           18,562               18,905            18,396
     outstanding-diluted
</TABLE>


        See accompanying notes to these unaudited financial statements.

                                      -4-
<PAGE>
 
                       PHARMACOPEIA, INC. AND SUBSIDIARY
                     CONSOLIDATED STATEMENTS OF CASH FLOWS
                            (DOLLARS IN THOUSANDS)
                                        


<TABLE>
<CAPTION>
                                                                      NINE MONTHS ENDED SEPTEMBER 30,
                                                                         1998                  1997
                                                               ------------------------------------------         
                                                                               (UNAUDITED)
<S>                                                              <C>                    <C>
CASH FLOWS FROM OPERATING ACTIVITIES
   Net loss                                                                  $(11,249)           $ (2,568)
   Adjustments to reconcile net loss to net cash
      (used in) operating activities:
      Depreciation and amortization                                             3,491               3,982
      Equity in undistributed earnings of joint venture                         1,013                 (52)
      Changes in assets and liabilities:
           Accounts receivable                                                  3,090               6,150
           Prepaid expenses and other current assets                            2,341                 299
           Other assets                                                          (733)                358
           Accounts payable                                                      (639)                436
           Accrued liabilities                                                 (1,179)             (1,903)
           Deferred revenue                                                    (7,771)             (5,919)
           Other liabilities                                                    1,142                (218)
                                                               ------------------------------------------
              Net cash provided by (used in) operating                        
               activities                                                     (10,494)                565
 
CASH FLOWS FROM INVESTING ACTIVITIES
   Capital expenditures                                                        (3,492)             (5,426)
   Capitalized software development costs                                          20              (1,299)
   Purchase of marketable securities                                          (49,556)            (67,946)
   Proceeds from maturities of marketable securities                           76,925              64,933
                                                               ------------------------------------------
              Net cash provided by (used in) investing                         
               activities                                                      23,897              (9,738)
 
CASH FLOWS FROM FINANCING ACTIVITIES
   Net proceeds from issuance of common stock                                     864               4,568
   Payments on notes payable                                                   (1,535)             (1,143)
   Increase in capital lease obligations                                                              512
   Principal payments on capital leases                                          (155)               (289)
                                                               ------------------------------------------
             Net cash provided by (used in) financing                            
              activities                                                         (826)              3,648
 
    Exchange rate effects on cash                                                 376                (658)
                                                               ------------------------------------------
    Net decrease in cash and cash equivalents                                  12,953              (6,183)
    Cash and cash equivalents, beginning of period                             24,609              31,568
                                                               ------------------------------------------
    Cash and cash equivalents, end of period                                 $ 37,562            $ 25,385
                                                               ==========================================
 
SUPPLEMENTAL DISCLOSURE OF CASH FLOW INFORMATION:
      Cash paid during the period for:
              Interest                                                       $    323            $    218
              Income taxes                                                   $  2,019            $    822
</TABLE>

        See accompanying notes to these unaudited 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, Molecular Simulations
Incorporated, ("MSI") was acquired by the Company on June 12, 1998 (see Note 3).
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 and the Company's Registration Statement on Form S-4
(Registration No. 333-47475).


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 and does not include any other potentially dilutive
securities.


NOTE (3) -- MOLECULAR SIMULATIONS INCORPORATED ACQUISITION

     On June 12, 1998, the Company completed its merger with MSI. In connection
with the merger, the Company exchanged approximately 7.1 million shares of its
Common Stock for all of the issued and outstanding MSI Common Stock, MSI Class B
Common Stock and MSI Series A Convertible Preferred Stock. The Company believes
this merger qualifies as a tax-free reorganization. This merger was accounted
for as a pooling-of-interests. Accordingly, the Company's financial statements
have been restated for all periods presented to include MSI. In connection with
the transaction, the Company recorded merger related charges of approximately
$8.0 million in the second quarter of 1998. Such charges consist of transaction
costs, principally investment banking and professional fees which must be
expensed under the pooling-of-interests method of accounting.

                                      -6-
<PAGE>
 
     The following table summarizes 1998 information on a separate company basis
for Pharmacopeia and MSI prior to completion of the merger.

<TABLE>
<CAPTION>
                                                    PERIOD FROM                     PERIOD FROM
                                                 APRIL 1, 1998 TO                JANUARY 1, 1998 TO
                                                   JUNE 12, 1998                   JUNE 12, 1998
                                          ----------------------------     ---------------------------
<S>                                         <C>                              <C>
Total revenue:
     Pharmacopeia                                    $ 5,890                         $12,322
     MSI                                               6,137                          20,437
 
Net income (loss):
     Pharmacopeia                                    $(1,362)                        $(3,588)
     MSI                                              (3,007)                         (1,483)
</TABLE>

NOTE (4) -- MARKETABLE SECURITIES

     As a result of the Company's merger with MSI (see Note 3) which was
completed on June 12, 1998, the Company anticipates that it's working capital
needs may fluctuate from month to month. Accordingly, as of June 30, 1998, the
Company transferred the classification of its marketable securities from 
held-to-maturity to available-for-sale. The estimated fair value of the
marketable securities approximates cost as of September 30, 1998 and, therefore,
no unrealized gains or losses existed at September 30, 1998.

NOTE (5) -- REPORTING COMPREHENSIVE INCOME

     As of January 1, 1998, the Company adopted Statement of Financial
Accounting Standards No. 130, "Reporting Comprehensive Income" ("SFAS No. 130").
SFAS No. 130 establishes new rules for the reporting and display of
comprehensive income and its components. The adoption of SFAS No. 130 had no
impact on the Company's results of operation or stockholders' equity. SFAS No.
130 requires foreign currency gains or losses, which prior to adoption were
reported separately in stockholder's equity, to be included in other
comprehensive income. The components of comprehensive income (loss) for the
three and nine month periods ended September 30, are as follows:

<TABLE>
<CAPTION>
                                                  THREE MONTHS ENDED                  NINE MONTHS ENDED
                                                    SEPTEMBER 30,                       SEPTEMBER 30,
                                          -------------------------------     -------------------------------
                                               1998              1997               1998              1997
                                          ------------     --------------     -------------     -------------
<S>                                         <C>              <C>                <C>               <C>
Net loss                                       $(2,083)           $(1,524)         $(11,249)          $(2,568)
Foreign currency gain (loss)                       382               (129)              376              (658)
                                          ------------     --------------     -------------     -------------
Total comprehensive (loss)                     $(1,701)           $(1,653)         $(10,873)          $(3,226)
                                          ============     ==============     =============     =============
</TABLE>

                                      -7-
<PAGE>
 
NOTE (6) -- IMPACT OF RECENTLY ISSUED ACCOUNTING STANDARDS

     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 MSI.

Item 2.  MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
         OF OPERATIONS

OVERVIEW

     The Company's financial statements for all periods presented have been
restated to include the operations of MSI.  The MSI merger was completed on June
12, 1998 and was accounted for as a pooling-of-interests. The acquisition of MSI
was completed by merging Micro Acquisition Corporation ("Micro") a wholly-owned
subsidiary of Pharmacopeia, with and into MSI, pursuant to an Agreement and Plan
of Merger and Reorganization dated as of February 4, 1998 by and among
Pharmacopeia, MSI and Micro.  Upon the merger of Micro with and into MSI, each
outstanding share of MSI Common Stock, MSI Class B Common Stock and MSI Series A
Convertible Preferred Stock was converted into 0.5292 shares of Pharmacopeia
common stock.

     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.  MSI was
incorporated in June 1994 and develops and commercializes molecular modeling,
simulation, and informatics software and services.

RESULTS OF OPERATIONS

THREE AND NINE MONTHS ENDED SEPTEMBER 30, 1998 AND 1997

     Contract revenue for the three and nine months ended September 30, 1998
increased to $7.0 million and $20.4 million, respectively, compared to $5.2
million and $16.8 million for the comparable periods in 1997.  The three and
nine month year to year increases primarily reflect expanded efforts in the
Schering-Plough, Bristol-Myers Squibb and Novartis collaborations.

                                      -8-
<PAGE>
 
     Software license, service and other revenue for the three and nine months
ended September 30, 1998 increased to $12.3 million and $36.8 million,
respectively, compared to $10.8 million and $33.1 million for the three and nine
months ended September  30, 1997.  The increases of $1.5 million, or 13%, and
$3.7 million, or 11%, respectively, are primarily the result of consolidating,
in 1998, the operating results of TMSI, the existing joint venture between MSI
and Teijin as a result of MSI becoming the controlling partner in the joint
venture.

     Research and development expenses increased to $12.2 million and $35.3
million for the three and nine months ended September 30, 1998, respectively,
compared to $10.3 million and $30.6 million for the corresponding periods in
1997. The increases of $1.9 million, or 18% and $4.7 million, or 15%,
respectively, primarily reflect increased spending on proprietary research and
development as Pharmacopeia continues to invest in internal discovery programs,
ultra high-throughput 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.

     Sales, general and administrative expenses increased to $9.2 million and
$26.1 million for the three and nine months ended September 30, 1998,
respectively, compared to $7.4 million and $21.8 million for the corresponding
periods in 1997. The increases of $1.8 million, or 23% and $4.3 million, or 20%,
respectively, are primarily attributable to consolidating, in 1998, the
operating results of TMSI along with increased payroll and personnel expenses as
the Company continued to hire additional sales, marketing and administrative
personnel.

     Merger related costs of $8.0 million were recorded for the nine months
ended September 30, 1998 in connection with the MSI merger. Such charges consist
of transaction costs, principally investment banking and professional fees which
must be expensed under the pooling-of-interests method of accounting.

     The Company had interest and other income of $1.1 million and $3.0 million
for the three and nine months ended September 30, 1998, respectively, compared
to $1.3 million and $3.6 million for the comparable periods in 1997. The
decreases of $0.2 million, or 19%, and $0.6 million, or 16%, respectively,
resulted primarily from a decrease in the average balance of cash, cash
equivalents and marketable securities.

     The Company recorded a provision for income taxes of $0.6 million for the
three months ended September 30, 1998 as compared to a provision for income
taxes of $0.5 million for the three months ended September 30, 1997.  The
Company recorded a provision of income taxes of $0.5 million for the nine months
ended September 30, 1998 as compared to a provision for income taxes of $1.8
million for the nine months ended September 30, 1997. The year to year favorable
tax variances are the result of the combined companies' ability to offset MSI's
taxable income with Pharmacopeia's losses during the period following the
completion of the merger.

                                      -9-
<PAGE>
 
LIQUIDITY AND CAPITAL RESOURCES

     As of September 30, 1998, the Company had working capital of $55.7 million.
The Company has funded its activities through September 30, 1998 primarily
through the sale of equity securities, funding under collaborative arrangements,
and sales of software licenses and hardware.

     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. As of September 30, 1998, the Company's cash and cash
equivalents totaled $37.6 million.  In addition, the Company had marketable
securities of $45.7 million.

     In addition, as of September 30, 1998, the Company had outstanding
commitments for construction and equipment purchases totaling $0.3 million.  The
Company anticipates that its capital requirements will continue to increase 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 has conducted a review of its products and the computer
programs that it uses internally to identify the systems that could be affected
by the "Year 2000" issue.  The Company presently believes that the Year 2000
problem will not pose significant operational problems for the Company's
products that it markets commercially or the computer programs that it currently
uses internally, and that the Company will not incur significant costs as a
result of the Year 2000 problem.

     The Company is in the the process of querying its customers, suppliers and
other service providers to determine whether they may experience any Year 2000
issues that may affect the Company. To date, the Company is not aware of any
such Year 2000 issue that would materially impact the Company's results of
operations, liquidity, or capital resources.  However, the Company has no means
of ensuring that third parties will be Year 2000 ready.  The inability of third
parties to complete their Year 2000 resolution process in a timely fashion could
materially impact the Company.  The effect of non-compliance by third parties is
not determinable.

     The Company anticipates that its existing capital resources will be
adequate to fund the Company's operations at least through 2000.  There can be
no assurance that changes will not occur that would consume available capital
resources before such time.  The Company's capital 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.

                                      -10-
<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.
10.13(b)****            Third Amendment to Lease Agreement dated March 31, 1996 between Pharmacopeia and
                        Eastpark at 8A.
</TABLE>

                                      -11-
<PAGE>
 
<TABLE>
<C>                    <S>
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.
10.19************#      Employment Agreement, dated January 30, 1998, between the Company and Richard Walsh
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.
10.27***********#       Employment Agreement effective November 30, 1995 between Molecular Simulations
                        Incorporated and Michael J. Savage
10.27(a)************#   Amendment No. 1 to Employment Agreement between Molecular Simulations Incorporated and
                        Michael J. Savage dated as of October 1, 1997
10.28***********#       Employment Agreement effective November 30, 1995 between Molecular Simulations
                        Incorporated and Saiid Zarrabian
10.28(a)************#   Amendment No. 1 to Employment Agreement between Molecular Simulations Incorporated and
                        Saiid Zarrabian dated as of October 1, 1997
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.
</TABLE>

                                      -12-
<PAGE>
 
<TABLE>
<C>                   <S>
10.34**********+        Collaboration and License Agreement between Pharmacopeia, Inc. and Bristol-Myers Squibb
                        Company dated November 26, 1997.
10.35************+      Joint Venture Agreement dated February 14, 1992 between Polygen Corporation and Teijin
                        Limited.
10.36************       Amendment No. 1 to Joint Venture Agreement dated March 30, 1998 between Teijin Limited
                        and Molecular Simulations Incorporated.
10.37************+      Distributorship Agreement dated April 1, 1992 between Polygen Corporation and Teijin
                        Molecular Simulations Incorporated
10.38************       Amendment to Distributorship Agreement dated October 17, 1994 between Molecular
                        Simulations Incorporated and Teijin Molecular Simulations Incorporated.
10.39************+      Amendment No. 2 to Distributorship Agreement dated September 30, 1996 between Molecular
                        Simulations Incorporated and Teijin Molecular Simulations Incorporated.
10.40++                 Amended and Restated Distributorship Agreement, dated March 1, 1998, between Molecular
                        Simulations Incorporated and Teijin Molecular Simulations Incorporated
10.41                   Indemnity Agreement, dated March 1, 1998, between Molecular Simulations Incorporated
                        and Teijin Molecular Simulations Incorporated
10.42                   Lease Agreement, dated February 26, 1987, as amended, between Sorrento Tech Limited and
                        Biosym Technologies, Inc.
11.1*                   Statement re Computation of Per Share Earnings.
27.1                    Financial Data Schedule
27.2                    Restated Financial Data Schedule as of September 30, 1997
</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.
   *** 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.  
   *********** Incorporated by reference to Exhibit 10.15 and 10.16 to Molecular
   Simulations Incorporated's Registration Statement on Form S-1 (Registration
   No. 333-21427) listed on February 10, 1997.
   ************ Incorporated by reference to the same numbered exhibit filed
   with the Company's Form 10-Q for the quarter ended June 30, 1998.  
   + Confidential treatment granted. 
   ++ Confidential treatment requested. 
   # Represents a management contract or compensatory plan or arrangement.

                                      -13-
<PAGE>
 
(b)  REPORTS ON FORM 8-K

     None.

                                      -14-
<PAGE>
 
                                   SIGNATURE


     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: November 13, 1998

                                      -15-
<PAGE>
 
                              PHARMACOPEIA, INC.
                               INDEX TO EXHIBITS



<TABLE>
<CAPTION>

    EXHIBIT NUMBER      Exhibit Name                                                      Page
<C>                     <S>                                                          <C>
        10.40           Amended and Restated Distributorship Agreement, dated
                        March 1, 1998, between Molecular Simulations Incorporated
                        and Teijin Molecular Simulations Incorporated.
        10.41           Indemnity Agreement, dated March 1, 1998, between
                        Molecular Simulations Incorporated and Teijin Molecular
                        Simulations Incorporated
        10.42           Lease Agreement, dated February 26, 1987, as amended,
                        between Sorrento Tech Limited and Biosym Technologies, Inc.
        27.1            Financial Data Schedule
        27.2            Restated Financial Data Schedule as of September 30, 1997
</TABLE>

                                      -16-