**Exhibit 31.1**

 

**CERTIFICATION OF CHIEF EXECUTIVE OFFICER**

 

(Pursuant to Rule 13a-14 of the

Securities Exchange Act of 1934, as amended,

as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of2002)

 

I,Mark J. Emkjer, certify that:

 

1.             I have reviewed this quarterly report on Form10-Q of Accelrys, Inc.;

 

2.             Based on my knowledge, this report does notcontain any untrue statement of a material fact or omit to state a materialfact necessary to make the statements made, in light of the circumstances underwhich such statements were made, not misleading with respect to the periodcovered by this report;

 

3.             Based on my knowledge, the financialstatements, and other financial information included in this report, fairlypresent in all material respects the financial condition, results of operationsand cash flows of the registrant as of, and for, the periods presented in thisreport;

 

4.             The registrant’s other certifying officer andI are responsible for establishing and maintaining disclosure controls and procedures(as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal controlover financial reporting (as defined in Exchange Act Rules 13a-15(f) and15d-15(f)) for the registrant and have:

 

a)             Designed such disclosure controls andprocedures, or caused such disclosure controls and procedures to be designedunder our supervision, to ensure that material information relating to theregistrant, including its consolidated subsidiaries, is made known to us byothers within those entities, particularly during the period in which thisreport is being prepared;

 

b)            Designed such internal control over financialreporting, or caused such internal control over financial reporting to bedesigned under our supervision, to provide reasonable assurance regarding thereliability of financial reporting and the preparation of financial statementsfor external purposes in accordance with generally accepted accountingprinciples;

 

c)             Evaluated the effectiveness of the registrant’sdisclosure controls and procedures and presented in this report our conclusionsabout the effectiveness of the disclosure controls and procedures, as of theend of the period covered by this report based on such evaluation; and

 

d)            Disclosed in this report any change in theregistrant’s internal control over financial reporting that occurred during theregistrant’s most recent fiscal quarter that has materially affected, or isreasonably likely to materially affect, the registrant’s internal control overfinancial reporting; and

 

5.             The registrant’s other certifying officer andI have disclosed, based on our most recent evaluation of internal control overfinancial reporting, to the registrant’s auditors and the audit committee ofthe registrant’s board of directors (or persons performing the equivalentfunctions):

 

a)             All significant deficiencies and materialweaknesses in the design or operation of internal control over financialreporting which are reasonably likely to adversely affect the registrant’sability to record, process, summarize and report financial information; and

 

b)            Any fraud, whether or not material, thatinvolves management or other employees who have a significant role in theregistrant’s internal control over financial reporting.

 

Date:  May 24, 2006

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

 

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