**Exhibit 31.1**

 

**CERTIFICATION OF PRINCIPAL EXECUTIVE OFFICER**

 

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

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

 

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

 

1.                                       I have reviewed this quarterly report on Form10-Q of Pharmacopeia Drug Discovery, Inc.;

 

2.                                       Based on my knowledge, this report does notcontain any untrue statement of a material fact or omit to state a materialfact necessary to make the statements made, in light of the circumstances underwhich such statements were made, not misleading with respect to the periodcovered by this quarterly report;

 

3.                                       Based on my knowledge, the financialstatements, and other financial information included in this quarterly report,fairly present in all material respects the financial condition, results ofoperations and cash flows of the registrant as of, and for, the periodspresented in this quarterly report;

 

4.                                       The registrant’s other certifying officer andI are responsible for establishing and maintaining disclosure controls andprocedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) for theregistrant and have:

 

a)                                      designed such disclosure controls andprocedures, or caused such disclosure controls and procedures to be designedunder our supervision, to ensure that material information relating to theregistrant is made known to us by others within those entities, particularlyduring the period in which this quarterly report is being prepared;

 

b)                                     evaluated the effectiveness of theregistrant’s disclosure controls and procedures and presented in this reportour conclusions about the effectiveness of the disclosure controls andprocedures, as of the end of the period covered by this report based on such evaluation;and

 

c)                                      disclosed in this report any change in theregistrant’s internal control over financial reporting that occurred during theregistrant’s most recent fiscal quarter that has materially affected, or isreasonably likely to materially affect, the registrant’s internal control overfinancial reporting; and

 

5.                                       The registrant’s other certifying officer andI have disclosed, based on our most recent evaluation of internal control overfinancial reporting, to the registrant’s auditors and the audit committee ofregistrant’s board of directors (or persons performing the equivalentfunctions):

 

a)                                      all significant deficiencies and materialweaknesses in the design or operation of internal control over financialreporting which are reasonably likely to adversely affect the registrant’sability to record, process, summarize and report financial information; and

 

b)                                     any fraud, whether or not material, thatinvolves management or other employees who have a significant role in theregistrant’s internal control over financial reporting.

 
| Date:  August 6, 2004 |                                                           |
|---------------------------------|----------------------------------------------------------------|
|                            |                                                           |
|                            | /s/ Joseph  A. Mollica                                    |   |
|                            | Joseph  A. Mollica, Ph.D.                                      |
|                            | Chairman  of the Board, President  and Chief Executive Officer |
|                            | (Principal  Executive Officer)                                 |

 

----