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                                                                   Exhibit 10.48

                              INDEMNITY AGREEMENT

     THIS AGREEMENT is made and entered into this 21st day of July, 1997 by and
between MOLECULAR SIMULATIONS INCORPORATED, a Delaware corporation (the
"Company"), and C. Peter W. Booth ("Agent").

                                   RECITALS

     WHEREAS, Agent performs a valuable service to the Company in his capacity
as Director of the Company;

     WHEREAS, the stockholders of the Company have adopted Amended and Restated
Bylaws (the "Bylaws") providing for the indemnification of the directors,
officers, employees and other agents of the Company, including persons serving
at the request of the Company in such capacities with other corporations or
enterprises, as authorized by the Delaware General Corporation Law, as amended
(the "Code");

     WHEREAS, the Bylaws and the Code, by their non-exclusive nature, permit
contracts between the Company and its agents, officers, employees and other
agents with respect to indemnification of such persons; and

     WHEREAS, in order to induce Agent to continue to serve as Director of the
Company, the Company has determined and agreed to enter into this Agreement with
Agent;

     NOW, THEREFORE, in consideration of Agent's continued service as Director
after the date hereof, the parties hereto agree as follows:

                                   AGREEMENT

     1.   SERVICES TO THE COMPANY. Agent will serve, at the will of the Company
or under separate contract, if any such contract exists, as Director of the
Company or as a director, officer or other fiduciary of an affiliate of the
Company (including any employee benefit plan of the Company) faithfully and to
the best of his ability so long as he is duly elected and qualified in
accordance with the provisions of the Bylaws or other applicable charter
documents of the Company or such affiliate; provided, however, that Agent may at
any time and for any reason resign from such position (subject to any
contractual obligation that Agent may have assumed apart from this Agreement)
and that the Company or any affiliate shall have no obligation under this
Agreement to continue Agent in any such position.

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     2.   INDEMNITY OF AGENT.  The Company hereby agrees to hold harmless and
indemnify Agent to the fullest extent authorized or permitted by the provisions
of the Bylaws and the Code, as the same may be amended from time to time (but,
only to the extent that such amendment permits the Company to provide broader
indemnification rights than the Bylaws or the Code permitted prior to adoption
of such amendment).

     3.   ADDITIONAL INDEMNITY.  In addition to and not in limitation of the
indemnification otherwise provided for herein, and subject only to the
exclusions set forth in Section 4 hereof, the Company hereby further agrees to
hold harmless and indemnify Agent:

          (A)  against any and all expenses (including attorneys' fees), witness
fees, damages, judgments, fines and amounts paid in settlement and any other
amounts that Agent becomes legally obligated to pay because of any claim or
claims made against or by him in connection with any threatened, pending or
completed action, suit or proceeding, whether civil, criminal, arbitrational,
administrative or investigative (including an action by or in the right of the
Company) to which Agent is, was or at any time becomes a party, or is threatened
to be made a party, by reason of the fact that Agent is, was or at any time
becomes a director, officer, employee or other agent of Company, or is or was
serving or at any time serves at the request of the Company as a director,
officer, employee or other agent of another corporation, partnership, joint
venture, trust, employee benefit plan or other enterprise; and

          (B)  otherwise to the fullest extent as may be provided to Agent by
the Company under the non-exclusivity provisions of the Code and Section 43 of
the Bylaws.

     4.   LIMITATIONS ON ADDITIONAL INDEMNITY.  No indemnity pursuant to Section
3 hereof shall be paid by the Company:

          (A)  on account of any claim against Agent for an accounting of
profits made from the purchase or sale by Agent of securities of the Company
pursuant to the provisions of Section 16(b) of the Securities Exchange Act of
1934 and amendments thereto or similar provisions of any federal, state or local
statutory law;

          (B)  on account of Agent's conduct that was knowingly fraudulent or
deliberately dishonest or that constituted willful misconduct;

          (C)  on account of Agent's conduct that constituted a breach of
Agent's duty of loyalty to the Company or resulted in any personal profit or
advantage to which Agent was not legally entitled;

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          (D)  for which payment is actually made to Agent under a valid and
collectible insurance policy or under a valid and enforceable indemnity clause,
bylaw or agreement, except in respect of any excess beyond payment under such
insurance, clause, bylaw or agreement;

          (E)  if indemnification is not lawful (and, in this respect, both the
Company and Agent have been advised that the Securities and Exchange Commission
believes that indemnification for liabilities arising under the federal
securities laws is against public policy and is, therefore, unenforceable and
that claims for indemnification should be submitted to appropriate courts for
adjudication); or

          (F)  in connection with any proceeding (or part thereof) initiated by
Agent, or any proceeding by Agent against the Company or its directors,
officers, employees or other agents, unless (i) such indemnification is
expressly required to be made by law, (ii) the proceeding was authorized by the
Board of Directors of the Company, (iii) such indemnification is provided by the
Company, in its sole discretion, pursuant to the powers vested in the Company
under the Code, or (iv) the proceeding is initiated pursuant to Section 9
hereof.

     5.   CONTINUATION OF INDEMNITY.  All agreements and obligations of the
Company contained herein shall continue during the period Agent is a director,
officer, employee or other agent of the Company (or is or was serving at the
request of the Company as a director, officer, employee or other agent of
another corporation, partnership, joint venture, trust, employee benefit plan or
other enterprise) and shall continue thereafter so long as Agent shall be
subject to any possible claim or threatened, pending or completed action, suit
or proceeding, whether civil, criminal, arbitrational, administrative or
investigative, by reason of the fact that Agent was serving in the capacity
referred to herein.

     6.   PARTIAL INDEMNIFICATION.  Agent shall be entitled under this Agreement
to indemnification by the Company for a portion of the expenses (including
attorneys' fees), witness fees, damages, judgments, fines and amounts paid in
settlement and any other amounts that Agent becomes legally obligated to pay in
connection with any action, suit or proceeding referred to in Section 3 hereof
even if not entitled hereunder to indemnification for the total amount thereof,
and the Company shall indemnify Agent for the portion thereof to which Agent is
entitled.

     7.   NOTIFICATION AND DEFENSE OF CLAIM.  Not later than thirty (30) days
after receipt by Agent of notice of the commencement of any action, suit or
proceeding, Agent will, if a claim in respect thereof is to be made against the
Company under this Agreement, notify the Company of the commencement thereof;
but the omission so to notify the Company will not relieve it from any liability
which it may have to Agent 

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otherwise than under this Agreement. With respect to any such action, suit or
proceeding as to which Agent notifies the Company of the commencement thereof:

          (A)  the Company will be entitled to participate therein at its own
expense;

          (B)  except as otherwise provided below, the Company may, at its
option and jointly with any other indemnifying party similarly notified and
electing to assume such defense, assume the defense thereof, with counsel
reasonably satisfactory to Agent. After notice from the Company to Agent of its
election to assume the defense thereof, the Company will not be liable to Agent
under this Agreement for any legal or other expenses subsequently incurred by
Agent in connection with the defense thereof except for reasonable costs of
investigation or otherwise as provided below. Agent shall have the right to
employ separate counsel in such action, suit or proceeding but the fees and
expenses of such counsel incurred after notice from the Company of its
assumption of the defense thereof shall be at the expense of Agent unless (i)
the employment of counsel by Agent has been authorized by the Company, (ii)
Agent shall have reasonably concluded that there may be a conflict of interest
between the Company and Agent in the conduct of the defense of such action or
(iii) the Company shall not in fact have employed counsel to assume the defense
of such action, in each of which cases the fees and expenses of Agent's separate
counsel shall be at the expense of the Company. The Company shall not be
entitled to assume the defense of any action, suit or proceeding brought by or
on behalf of the Company or as to which Agent shall have made the conclusion
provided for in clause (ii) above; and

          (C)  the Company shall not be liable to indemnify Agent under this
Agreement for any amounts paid in settlement of any action or claim effected
without its written consent, which shall not be unreasonably withheld. The
Company shall be permitted to settle any action except that it shall not settle
any action or claim in any manner which would impose any penalty or limitation
on Agent without Agent's written consent which may be given or withheld in
Agent's sole discretion.

          8.   EXPENSES.  The Company shall advance, prior to the final
disposition of any proceeding, promptly following request therefor, all expenses
incurred by Agent in connection with such proceeding upon receipt of an
undertaking by or on behalf of Agent to repay said amounts if it shall be
determined ultimately that Agent is not entitled to be indemnified under the
provisions of this Agreement, the Bylaws, the Code or otherwise.

          9.   ENFORCEMENT.  Any right to indemnification or advances granted by
this Agreement to Agent shall be enforceable by or on behalf of Agent in any
court of competent jurisdiction if (i) the claim for indemnification or advances
is deemed, in whole or in part, or (ii) no disposition of such claim is made
within ninety (90) days of request therefor. Agent, in such enforcement action,
if successful in whole or in part, 

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shall be entitled to be paid also the expense of prosecuting his claim. It shall
be a defense to any action for which a claim for indemnification is made under
Section 3 hereof (other than an action brought to enforce a claim for expenses
pursuant to Section 8 hereof, provided that the required undertaking has been
tendered to the Company) that Agent is not entitled to indemnification because
of the limitations set forth in Section 4 hereof. Neither the failure of the
Company (including its Board of Directors or its stockholders) to have made a
determination prior to the commencement of such enforcement action that
indemnification of Agent is proper in the circumstances, nor an actual
determination by the Company (including its Board of Directors or its
stockholders) that such indemnification is improper shall be a defense to the
action or create a presumption that Agent is not entitled to indemnification
under this Agreement or otherwise.

     10.  SUBROGATION.  In the event of payment under this Agreement, the
Company shall be subrogated to the extent of such payment to all of the rights
of recovery of Agent, who shall execute all documents required and shall do all
acts that may be necessary to secure such rights and to enable the Company
effectively to bring suit to enforce such rights.

     11.  NON-EXCLUSIVITY OF RIGHTS.  The rights conferred on Agent by this
Agreement shall not be exclusive of any other right which Agent may have or
hereafter acquire under any statute, provision of the Company's Amended and
Restated Certificate of Incorporation or Bylaws, agreement, vote of stockholders
or directors, or otherwise, both as to action in his official capacity and as to
action in another capacity while holding office.

     12.  SURVIVAL OF RIGHTS.

          (A)  The rights conferred on Agent by this Agreement shall continue
after Agent has ceased to be a director, officer, employee or other agent of the
Company or to serve at the request of the Company as a director, officer,
employee or other agent of another corporation, partnership, joint venture,
trust, employee benefit plan or other enterprise and shall inure to the benefit
of Agent's heirs, executors and administrators.

          (B)  The Company shall require any successor (whether direct or
indirect, by purchase, merger, consolidation or otherwise) to all or
substantially all of the business or assets of the Company, expressly to assume
and agree to perform this Agreement in the same manner and to the same extent
that the Company would be required to perform if no such succession had taken
place.

     13.  SEPARABILITY.  Each of the provisions of this Agreement is a separate
and distinct agreement and independent of the others, so that if any provision
hereof shall be held to be invalid for any reason, such invalidity or
unenforceability shall not affect the validity or enforceability of the other
provisions hereof. Furthermore, if this Agreement 

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shall be invalidated in its entirety on any ground, then the Company shall
nevertheless indemnify Agent to the fullest extent provided by the Amended and
Restated Bylaws, the Code or any other applicable law.

     14.  ENTIRE AGREEMENT.  This Agreement and the agreements referenced herein
constitute the entire agreement between the parties hereto pertaining to the
subject matter hereof, and any and all other written or oral agreements existing
between the parties hereto pertaining to the subject matters hereof are
superseded and expressly canceled.

     15.  GOVERNING LAW.  This Agreement shall be interpreted and enforced in
accordance with the laws of the State of Delaware.

     16.  AMENDMENT AND TERMINATION.  No amendment, modification, termination or
cancellation of this Agreement shall be effective unless in writing signed by
both parties hereto.

     17.  IDENTICAL COUNTERPARTS.  This Agreement may be executed in one or more
counterparts, each of which shall for all purposes be deemed to be an original
but all of which together shall constitute but one and the same Agreement.  Only
one such counterpart need be produced to evidence the existence of this
Agreement.

     18.  HEADINGS.  The headings of the sections of this Agreement are inserted
for convenience only and shall not be deemed to constitute part of this
Agreement or to affect the construction hereof.

     19.  NOTICES.  All notices, requests, demands and other communications
hereunder shall be in writing and shall be deemed to have been duly given (i)
upon delivery if delivered by hand to the party to whom such communication was
directed or (ii) upon the third business day after the date on which such
communication was mailed if mailed by certified or registered mail with postage
prepaid:

          (A)  If to Agent, at the address indicated on the signature page
hereof.

          (B)  If to the Company, to

                    Molecular Simulations Incorporated
                    9685 Scranton Road
                    San Diego, CA 92121

or to such other address as may have been furnished to Agent by the Company.

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IN WITNESS WHEREOF, the parties hereto have executed this Agreement on and as of
the day and year first above written.

                            MOLECULAR SIMULATIONS INCORPORATED


                            By: /s/ Michael J. Savage
                                -------------------------------------
                                MICHAEL J. SAVAGE
                                PRESIDENT AND CHIEF EXECUTIVE OFFICER



                            AGENT


                            /s/ C. Peter W. Booth
                            -----------------------------------------
                            Signature


                            /s/ C. Peter W. Booth
                            -----------------------------------------
                            Print Name

                            Address:

                            One Park Place
                            -----------------------------------------

                            Corning, N.Y.  14830
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