**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 of 2002)

 

I,Leslie J. Browne, Ph.D., certify that:

 

1.                                       I have reviewedthis quarterly report on Form 10-Q of Pharmacopeia DrugDiscovery, Inc.;

 

2.                                       Based on myknowledge, this report does not contain any untrue statement of a material factor omit to state a material fact necessary to make the statements made, inlight of the circumstances under which such statements were made, notmisleading with respect to the period covered by this quarterly report;

 

3.                                       Based on myknowledge, the financial statements, and other financial information includedin this quarterly report, fairly present in all material respects the financialcondition, results of operations and cash flows of the registrant as of, andfor, the periods presented in this quarterly report;

 

4.                                       The registrant’sother certifying officers and I are responsible for establishing andmaintaining disclosure controls and procedures (as defined in Exchange ActRules 13a-15(e) and 15d-15(e)) for the registrant and have:

 

a)                                      designed suchdisclosure controls and procedures, or caused such disclosure controls and proceduresto be designed under our supervision, to ensure that material informationrelating to the registrant is made known to us by others within the entity,particularly during the period in which this quarterly report is beingprepared;

 

b)                                     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

 

c)                                      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, the registrant’sinternal control over financial reporting; and

 

5.                                       The registrant’sother certifying officers and I have disclosed, based on our most recentevaluation of internal control over financial reporting, to the registrant’sauditors and the audit committee of 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 4, 2005 |                                             |
|-------------------------|--------------------------------------------------|
|                    |                                             |
|                    | /s/ Leslie  J. Browne, Ph.D.                |   |
|                    | Leslie  J. Browne, Ph.D.                         |
|                    | President,  Chief Executive Officer and Director |
|                    | (Principal  Executive Officer)                   |

 

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