Exhibit 10.1

                              AMENDED AND RESTATED
                      SECURED PROMISSORY NOTE AND AGREEMENT
                             ("Note and Agreement")


$13,000,000.00                                                New York, New York
                                               Originally issued October 8, 2001
                                           Amended and restated October 24, 2001

FOR VALUE RECEIVED, Axys Pharmaceuticals, Inc., a Delaware corporation
("Borrower"), hereby promises to pay to the order of PE Corporation (NY), a New
York corporation ("Lender"), the principal sum of THIRTEEN MILLION DOLLARS
($13,000,000) or such lesser amount as shall equal the outstanding principal
amount of all sums advanced to Borrower hereunder and to pay interest on the
outstanding balance of said sum at a rate equal to the Prime Rate (as defined
below) plus one percent (1%) per annum. All then outstanding principal and
accrued interest hereunder shall be due and payable in full upon the earliest of
(a) a sale of all or substantially all of the assets of the Borrower (determined
on a consolidated basis) to any person or entity (other than Lender or an
affiliate of Lender); (b) a Change in Control (as defined below); (c) the
closing of any public or private offering of capital stock or debt securities of
Borrower or any other equity or debt financing that yields net proceeds to
Borrower in excess of $13,000,000; (d) any fee becoming payable to Applera
Corporation pursuant to Section 8.02 of the Agreement and Plan of Merger dated
June 12, 2001 among Applera Corporation, Angel Acquisition Sub, Inc. and the
Borrower (the "Merger Agreement"); (e) the hundred and twentieth (120th) day
following any other termination of the Merger Agreement pursuant to the terms
thereof; and (f) June 15, 2002 (the "Maturity Date"). The events described in
items (a) through (f) above are collectively referred to herein as "Note
Termination Events". As used herein, "Change of Control" means any person or
entity becomes the beneficial owner (within the meaning of Rule 13d-3 of the
rules and regulations of the Securities and Exchange Commission promulgated
under the Securities Exchange Act of 1934, as amended) of fifteen percent (15%)
or more of the outstanding common stock of Borrower other than as contemplated
by the Merger Agreement.

     1. Payments. Borrower shall make all payments hereunder for the account of
        Lender at Citibank, N.A., New York, New York, ABA# 021000089, Credit PE
        Corporation, Account #_____________, or to such other address as Lender
        shall notify Borrower, in lawful money of the United States and in same
        day or immediately available funds not later than 12:00 noon (New York
        City time) on the date due, or as otherwise agreed to by Lender.

     2. Prepayments. Notwithstanding anything to the contrary herein, Borrower
        shall have the right at any time and from time to time to prepay any
        amounts due hereunder in whole or in part in minimum multiples of
        $500,000 without penalty upon two (2) business days prior written notice
        to Lender.

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     3. Interest. All computations of interest under this Note and Agreement
        shall be based on a year of 365 or 366 days, as applicable, for actual
        days elapsed. In the event that, contrary to the intent of Lender and
        Borrower, Borrower pays interest under this Note and Agreement and it is
        determined that such interest rate was in excess of the then legal
        maximum rate, then that portion of the interest payment representing an
        amount in excess of the then legal maximum rate shall be deemed a
        payment of principal and applied against the principal then due under
        this Note and Agreement. For purposes of this Note, the "Prime Rate"
        shall be defined as the rate of interest per annum publicly announced
        from time to time by Citibank, N.A. as its prime rate in effect at its
        principal office in New York, and each change in the Prime Rate shall be
        effective from and including the date such change is publicly announced
        as being effective.


     4. Pledge Agreement. This Note and Agreement is secured by certain
        collateral more specifically described in the Schedules hereto and in
        the Pledge Agreement dated October 8, 2001 between Borrower and Lender
        (as may be amended from time to time, the "Pledge Agreement").

     5. Conditions to Advances, Use of Proceeds, Covenants. Amounts shall be
        advanced to Borrower under this Note and Agreement solely in accordance
        with the terms and conditions set forth in this Note and Agreement,
        including the Schedules attached hereto and incorporated herein by
        reference. Borrower shall use the proceeds of any amount advanced under
        this Note and Agreement solely for the purposes set forth in the
        Schedules hereto or the applicable Borrowing Request. Until the
        termination of this Note and Agreement and payment in full by Borrower
        or forgiveness by Lender of all amounts outstanding under this Note and
        Agreement, Borrower agrees that it shall (i) comply with and duly
        perform all of its covenants, obligations and agreements set forth in
        the Merger Agreement, so long as such agreement remains in full force
        and effect, and the Pledge Agreement, which are hereby incorporated
        mutatis mutandis herein by reference as if fully set forth herein; (ii)
        comply with all of its covenants, obligations and agreements set forth
        in Sections 4.01(a), (d), (e), (f), (g) and (i) of the Merger Agreement,
        regardless of whether the Merger Agreement remains in full force and
        effect; and (iii) not incur any Indebtedness (as defined in the Merger
        Agreement) for borrowed money or guarantee any such Indebtedness of
        another person or entity or enter into any arrangement having the
        economic effect of the foregoing except as expressly set forth in
        Section 4.01(f) of the Company Disclosure Schedule (as defined in the
        Merger Agreement).

     6. Representations and Warranties. Borrower represents and warrants to
        Lender that as of the date hereof and as of any Advance Date (as defined
        in Schedule A hereto):

            a)  Borrower is a corporation duly organized, validly existing and
                in good standing under the laws of the jurisdiction of its
                incorporation and has all requisite corporate power and
                authority to execute, deliver and perform its obligations under
                this Note and Agreement and the Pledge Agreement.

            b)  The execution, delivery and performance by Borrower of this Note
                and Agreement and the Pledge Agreement have been duly authorized
                by all necessary


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                corporate action of Borrower, and each of this Note and
                Agreement and the Pledge Agreement constitutes the legal, valid
                and binding obligation of Borrower, enforceable against Borrower
                in accordance with its terms.

            c)  No authorization, consent, approval, license, exemption of, or
                filing or registration with, any governmental authority or
                agency, or approval or consent of any other person or entity, is
                required for the due execution, delivery or performance by
                Borrower of this Note and Agreement or the Pledge Agreement
                except for the Required Consent in the case of the Pledge
                Agreement and Other Advances under the Note and Agreement.

            d)  The representations and warranties made by the Borrower (i) in
                the Pledge Agreement are true and correct as of such date and
                (ii) in Article II of the Merger Agreement (x) that are
                qualified as to "Company Material Adverse Effect" (as such term
                is defined in the Merger Agreement) are true and correct as of
                such date and (y) that are not so qualified are true and correct
                in all material respect as of such date, except for those
                representations and warranties in Article II of the Merger
                Agreement which address matters only as of a particular date
                (which shall have been true and correct as of such date).

     7. Events of Default. The occurrence of any one or more of the following
        events shall constitute an "Event of Default" hereunder:

            a)  Borrower shall fail to pay any then outstanding principal when
                due or any interest or other amount payable under this Note and
                Agreement within five (5) business days of when due; or

            b)  Borrower shall fail in any material respect to perform any of
                its other covenants, obligations or agreements contained in this
                Note and Agreement, the Pledge Agreement or the Merger
                Agreement, so long as such agreement remains in full force and
                effect, and such failure shall continue for ten (10) business
                days after written notice thereof by Lender; or

            c)  Any representation, warranty, certificate, or other statement
                (financial or otherwise) made, deemed made or furnished by or on
                behalf of Borrower in writing to Lender in connection with this
                Note and Agreement, the Pledge Agreement or the Merger
                Agreement, so long as such agreement remains in full force and
                effect, or as an inducement to Lender to advance the sums under
                this Note and Agreement, shall have been false or incorrect in
                any material respect when made or deemed made; or

            d)  Borrower (i) shall fail to make any payment when due under the
                terms of any bond, debenture, note or other evidence of
                indebtedness, if any, individually in excess of $100,000 to be
                paid by Borrower, and such failure shall continue beyond any
                period of grace provided with respect thereto or (ii) shall
                default in the observance or performance of any other agreement,
                term or condition


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                contained in any such bond, debenture, note or other evidence of
                indebtedness providing for principal payments in excess of
                $100,000; or

            e)  The holder or holders of any bond, debenture, note or other
                evidence of indebtedness of Borrower providing for principal
                payments in excess of $100,000 shall accelerate such
                indebtedness to become due prior to its stated date of maturity;
                or

            f)  Borrower shall (i) apply for or consent to the appointment of a
                receiver, trustee, liquidator or custodian of itself or of all
                or any part of its property; (ii) admit in writing its inability
                to pay its debts generally as they mature; (iii) make a general
                assignment for the benefit of its or any of its creditors; (iv)
                be dissolved or liquidated in full or in part; (v) become
                insolvent (as such term may be defined or interpreted under any
                applicable statute); (vi) commence a voluntary case or other
                proceeding seeking liquidation, reorganization or other relief
                with respect to itself or its debts under any bankruptcy,
                insolvency or other similar law now or hereafter in effect or
                consent to any such relief or to the appointment of or taking
                possession of its property by any official in an involuntary
                case or other proceeding commenced against it; or (vii) take any
                action for the purpose of effecting any of the foregoing; or

            g)  Proceedings for the appointment of a receiver, trustee,
                liquidator or custodian of Borrower or of all or any material
                part of its property, or an involuntary case or other
                proceedings seeking liquidation, reorganization or other relief
                with respect to Borrower or the debts thereof under any
                bankruptcy, insolvency or other similar law now or hereafter in
                effect, shall be commenced and an order for relief entered or
                such proceeding shall not be dismissed or discharged within
                sixty (60) days of commencement; or

            h)  A final judgment or final judgments for the payment of money,
                which individually or in the aggregate, exceed $250,000 in
                excess of the amount covered by insurance, shall be rendered
                against Borrower and the same shall remain undischarged for a
                period of thirty (30) days during which execution shall not be
                effectively stayed; or any judgment, writ, assessment, warrant
                of attachment, execution, levy or similar process shall be
                issued or levied against any material part of the property of
                Borrower and such judgment, writ, assessment, warrant of
                attachment, execution, levy or similar process shall not be
                released, stayed, vacated or otherwise dismissed within ten (10)
                days after issue or levy; or

            i)  This Note and Agreement or the Pledge Agreement shall cease to
                be, or be asserted by Borrower not to be, a legal, valid and
                binding obligation of Borrower, enforceable in accordance with
                its terms.

            Upon the occurrence or existence of any Event of Default, Lender may
            (A) at any time terminate any obligation to make loans or advance
            sums to Borrower under this Note and Agreement; (B) at any time
            declare all unpaid amounts owing or payable

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            under this Note and Agreement to be immediately due and payable
            without presentment, demand, protest or any other notice of any
            kind, all of which are hereby expressly waived by Borrower; and/or
            (C) exercise all rights and remedies available to Lender under this
            Note and Agreement, the Pledge Agreement or applicable law;
            provided, however, that upon the occurrence or existence of any
            Event of Default described in clause (f) or (g) above, immediately
            and without notice, (1) any obligation to make loans or advance sums
            to Borrower under this Note and Agreement shall automatically
            terminate and (2) all unpaid amounts owing or payable under this
            Note and Agreement shall automatically become immediately due and
            payable, without presentment, demand, protest or any other notice of
            any kind, all of which are hereby expressly waived by Borrower.




     8. General.

            a)  This Note and Agreement shall become effective as of the date
                hereof, provided that no Other Advance (as defined in Schedule A
                to this Note and Agreement) shall be made prior to the date (the
                "Pledge Effective Date") of receipt by Borrower of the consent
                of the holders of Borrower's 8% Senior Secured Convertible
                Notes due 2004 (the "Notes") to the extent required under the
                First Supplemental Indenture, dated as of September 22, 2000,
                between Borrower and U.S. Bank Trust National Association, as
                Trustee with respect to the Notes (the "Required Consent").

            b)  Borrower agrees to pay on demand all reasonable costs and
                expenses of Lender, and the reasonable fees and disbursements of
                counsel, in connection with the enforcement or attempted
                enforcement of, and preservation of any rights or interests
                under, this Note and Agreement, including in any out-of-court
                workout or other refinancing or restructuring or in any
                bankruptcy case. Any amounts payable to Lender pursuant to this
                Section 8(a) if not paid upon demand shall bear interest from
                the date of such demand until paid in full, at the rate of
                interest set forth herein in respect of principal outstanding
                hereunder.

            c)  If at any time any provision of this Note and Agreement is or
                becomes illegal, invalid or unenforceable in any respect,
                neither the legality, validity nor enforceability of the
                remaining provisions shall in any way be affected or impaired
                thereby.

            d)  Any term, covenant, agreement or condition of this Note and
                Agreement may be amended or waived if, in the case of an
                amendment, such amendment is in writing and is signed by
                Borrower and Lender and, in the case of a waiver, such waiver is
                in writing and is signed by the party waiving such term,
                covenant, agreement or condition. No failure or delay by Lender
                in exercising any right or remedy hereunder shall operate as a
                waiver thereof or of any other right or remedy nor shall any
                single or partial exercise of any such right or remedy preclude
                any other further exercise thereof or of any other right or
                remedy. The acceptance at any time by Lender of any past due
                amount hereunder shall not be deemed to be a waiver of the right
                to require prompt payment when due of any other amounts


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                then or thereafter due and payable. Unless otherwise specified
                in such waiver or consent, a waiver or consent given hereunder
                shall be effective only in the specific instance and for the
                specific purpose for which given.

            e)  This Note and Agreement shall be binding upon and inure to the
                benefit of Borrower, Lender, and their respective successors and
                permitted assigns, except that Borrower may not assign or
                transfer any of its rights or obligations under this Note and
                Agreement without the prior written consent of Lender. Prior to
                the occurrence of any Note Termination Event, Lender may at any
                time sell, assign, or otherwise transfer only to any of its
                affiliates or subsidiaries all or part of the obligations of
                Borrower and Lender under this Note and Agreement. After the
                occurrence of any Note Termination Event, Lender may at any time
                sell, assign, or otherwise transfer to any other person or
                entity all or part of the obligations of Borrower and Lender
                under this Note and Agreement.

            f)  Nothing expressed in or to be implied from this Note and
                Agreement is intended to give, or shall be construed to give,
                any person or entity, other than the parties hereto and their
                permitted successors and assigns hereunder, any benefit or legal
                or equitable right, remedy or claim under or by virtue of this
                Note and Agreement or under or by virtue of any provision
                herein.

            g)  The words "hereof," "herein," "hereunder" and similar words
                refer to this Note and Agreement as a whole (including the
                Schedules attached hereto) and not to any particular provision
                of this Note and Agreement.

            h)  Borrower hereby waives presentment, demand, protest, notice of
                dishonor and all other notices, except as expressly provided
                herein, any release or discharge arising from any extension of
                time, discharge of a prior party, or other cause of release or
                discharge other than actual payment in full hereof.

            i)  The section headings used in this Note and Agreement are for
                convenience of reference only and are not to affect the
                construction hereof or be taken into consideration in the
                interpretation hereof.

            j)  This Note and Agreement shall be construed in accordance with
                and governed by the laws of the State of New York.

                            [Signature Page Follows]



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IN WITNESS WHEREOF, the undersigned duly authorized officer of Borrower has
executed this Note and Agreement as of the date first set forth above.

                                         AXYS PHARMACEUTICALS, INC.



                                         By: /s/ Paul J. Hastings
                                            ------------------------------------
                                             Name: Paul J. Hastings
                                             Title: President & Chief Executive
                                                    Officer