**Exhibit 31.1**

 

**CERTIFICATION OF PRINCIPAL EXECUTIVE OFFICER**

 

(Pursuant to Rule 13a-14 of the Securities Exchange Act of 1934,as amended,

as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of2002)

 

I, Joseph A. Mollica, Ph.D., certify that:

 

1.             Ihave reviewed this quarterly report on Form 10-Q of Pharmacopeia DrugDiscovery, Inc.;

 

2.             Basedon my knowledge, this report does not contain any untrue statement of amaterial fact or omit to state a material fact necessary to make the statementsmade, in light of the circumstances under which such statements were made, notmisleading with respect to the period covered by this quarterly report;

 

3.             Basedon my knowledge, the financial statements, and other financial informationincluded in this quarterly report, fairly present in all material respects thefinancial condition, results of operations and cash flows of the registrant asof, and for, the periods presented in this quarterly report;

 

4.             Theregistrant’s other certifying officer and I are responsible for establishingand maintaining disclosure controls and procedures (as defined in Exchange ActRules 13a-15(e) and 15d-15(e)) for the registrant and have:

 

a)             designedsuch disclosure controls and procedures, or caused such disclosure controls andprocedures to be designed under our supervision, to ensure that materialinformation relating to the registrant is made known to us by others withinthose entities, particularly during the period in which this quarterly reportis being prepared;

 

b)            evaluatedthe effectiveness of the registrant’s disclosure controls and procedures andpresented in this report our conclusions about the effectiveness of thedisclosure controls and procedures, as of the end of the period covered by thisreport based on such evaluation; and

 

c)             disclosedin this report any change in the registrant’s internal control over financialreporting that occurred during the registrant’s most recent fiscal quarter thathas materially affected, or is reasonably likely to materially affect, theregistrant’s internal control over financial reporting; and

 

5.             Theregistrant’s other certifying officer and I have disclosed, based on our mostrecent evaluation of internal control over financial reporting, to theregistrant’s auditors and the audit committee of registrant’s board ofdirectors (or persons performing the equivalent functions):

 

a)             allsignificant deficiencies and material weaknesses in the design or operation ofinternal control over financial reporting which are reasonably likely to adverselyaffect the registrant’s ability to record, process, summarize and reportfinancial information; and

 

b)            anyfraud, whether or not material, that involves management or other employees whohave a significant role in the registrant’s internal control over financialreporting.

 
| Date:  June 2, 2004 |                                                          |
|--------------------------|---------------------------------------------------------------|
|                     |                                                          |
|                     | /s/ Joseph A. Mollica                                    |   |
|                     | Joseph A. Mollica, Ph.D.                                      |
|                     | Chairman of the Board, President  and Chief Executive Officer |
|                     | (Principal Executive Officer)                                 |

 

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