**Exhibit 31.1**

**CERTIFICATION OFCHIEF EXECUTIVE OFFICER**

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

I, Mark J. Emkjer, certify that:

1.      I have reviewed this quarterlyreport on Form 10-Q of Accelrys, Inc.;

2.      Based on my knowledge, this reportdoes not contain any untrue statement of a material fact or omit to state amaterial 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)           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 principles;

c)           Evaluatedthe effectiveness 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)          Disclosedin this 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 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 theequivalent 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)          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:  August 4,2006

 
|        |   | /s/ Mark J. Emkjer                    |   |   |
|--------|--------|---------------------------------------|--------|--------|
|   |   | Mark J. Emkjer                        |   |   |
|   |   | President and Chief Executive Officer |   |   |
|   |   | (Principal Executive Officer)         |   |   |

 

 

----