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**EXHIBIT 31.1**

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**CERTIFICATION OF CHIEF EXECUTIVE OFFICER PURSUANT TO**
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**SECTION 302 OF THESARBANES-OXLEY ACT OF 2002**

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I, John P. McAlister, certify that:

1.             I have reviewed this annualreport ("report") on Form 10-K of Tripos, 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.             The registrant's other certifyingofficer and I are responsible for establishing and maintaining disclosurecontrols 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 and have:

                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 report is being prepared;

                b)            designed suchinternal control 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)            evaluatedthe effectiveness of the registrant's disclosure controls and procedures andpresented in this report our conclusions about the effectiveness of the disclosurecontrols and procedures, as of the end of the period covered by this reportbased on such evaluation; and

                d)            disclosed in thisreport any change in the registrant's internal control over financial reportingthat occurred during the registrant's most recent fiscal quarter (theregistrant's fourth fiscal quarter in the case of an annual report) that hasmaterially affected, or is reasonably likely to materially affect, theregistrant's internal control over financial reporting; and

5.             The registrant's other certifyingofficer and I have disclosed, based on our most recent evaluation of internalcontrol over financial reporting, to the registrant's auditors and the auditcommittee of the registrant's board of directors (or persons performing the equivalentfunctions):

                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, whetheror not material, that involves management or other employees who have asignificant role in the registrant's internal control over financial reporting.

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Date:  April 11, 2006

 

     /s/John P. McAlister

     JohnP. McAlister 

    ChiefExecutive Officer

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