EXHIBIT31.1

** **

```
**CERTIFICATION OF CHIEF EXECUTIVE OFFICER PURSUANT TO**
```

**SECTION 302 OF THE SARBANES-OXLEY ACT OF2002**

** **

I,John P. McAlister, certify that:

1.         Ihave reviewed this quarterly report on Form 10-Q of Tripos, 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 report;

3.         Basedon my knowledge, the financial statements, and other financial informationincluded in this report, fairly present in all material respects the financialcondition, results of operations and cash flows of the registrant as of, and for,the periods presented in this 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)) and internal control over financial reporting(as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrantand 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, including its consolidatedsubsidiaries, is made known to us by others within those entities, particularlyduring the period in which this report is being prepared;

            b)         designedsuch internal control over financial reporting, or caused such internal controlover financial reporting to be designed under our supervision, to providereasonable assurance regarding the reliability of financial reporting and thepreparation of financial statements for external purposes in accordance withgenerally accepted accounting principals;

c)         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 suchevaluation; and

            d)         disclosedin this quarterly report any change in the registrant's internal control overfinancial reporting that occurred during the registrant's most recent fiscalquarter (the registrant's fourth fiscal quarter in the case of an annualreport) that has materially affected, or is reasonably likely to materiallyaffect, the registrant'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 the 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 toadversely affect the registrant's ability to record, process, summarize andreport financial 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:  November 14, 2006

 

     /s/ JohnP. McAlister

     John P.McAlister 

     ChiefExecutive Officer

----