**Exhibit 31.1**

 

**CERTIFICATIONOF PRINCIPAL EXECUTIVE OFFICER**

 

(Pursuant to Rule 13a-14(a) of theSecurities Exchange Act of 1934, as amended,as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002)

 

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

 

1.             I have reviewed thisquarterly report on Form 10-Q of Pharmacopeia, Inc.;

 

2.             Based on my knowledge, thisreport does not contain any untrue statement of a material fact or omit tostate a material fact necessary to make the statements made, in light of thecircumstances under which such statements were made, not misleading withrespect to the period covered by this report;

 

3.             Based on my knowledge, thefinancial statements, and other financial information included in this 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 report;

 

4.             Theregistrant’s other certifying officers and I are responsible for establishingand maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and15d-15(e)) and internal control over financial reporting (as defined inExchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant andhave:

 

a)             designed suchdisclosure controls and procedures, or caused such disclosure controls andprocedures to be designed under our supervision, to ensure that materialinformation relating to the registrant, including its consolidatedsubsidiaries, is made known to us by others within those entities, particularlyduring the period in which this quarterly report is being prepared;

 

b)            designed such internalcontrol over financial reporting, or caused such internal control overfinancial reporting to be designed under our supervision, to provide reasonableassurance regarding the reliability of financial reporting and the preparationof financial statements for external purposes in accordance with generallyaccepted accounting principles;

 

c)             evaluated theeffectiveness 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

 

d)            disclosed inthis 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.             The registrant’s othercertifying officers and I have disclosed, based on our most recent evaluationof internal control over financial reporting, to the registrant’s auditors andthe audit committee of the registrant’s board of directors (or personsperforming the equivalent functions):

 

a)             all significantdeficiencies and material weaknesses in the design or operation of internalcontrol over financial reporting which are reasonably likely to adverselyaffect the registrant’s ability to record, process, summarize and reportfinancial information; and

 

b)            any fraud,whether or not material, that involves management or other employees who have asignificant role in the registrant’s internal control over financial reporting.

 
| Date: November 6, 2008 |   |                                                                     |
|-----------------------------|--------|--------------------------------------------------------------------------|
|                        | By:    | /s/ Joseph A. Mollica, Ph.D.                                        |
|                        |   | Joseph A. Mollica, Ph.D.                                                 |
|                        |   | Chairman of the Board and  Interim President and Chief Executive Officer |
|                        |   | (Principal Executive Officer)                                            |

 

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