<PAGE>   1
                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549


                                    FORM 10-Q

[X]   QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
      EXCHANGE ACT OF 1934 For the Quarterly period ended September 30, 2000.

                                       or

[ ]   TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
      EXCHANGE ACT OF 1934 For the transition period from ________ to _________.



Commission File No. 000-31101


                        APPLIED MOLECULAR EVOLUTION, INC.
                        ---------------------------------
                          (Exact name of registrant as
                            specified in its charter)


          Delaware                                              33-0374014
   ----------------------                                  -------------------
(State or other jurisdiction of                             (I.R.S. Employer
incorporation or organization)                             Identification No.)


                               3520 Dunhill Street
                           San Diego, California 92121
                           ---------------------------
              (Address of principal executive offices and zip code)


                                 (858) 597-4990
                                 --------------
              (Registrant's telephone number, including area code)


Indicate by check mark whether the registrant (1) has filed all reports required
to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during
the preceding 12 months (or for such shorter period that the registrant was
required to file such reports), and (2) has been subject to such filing
requirements for the past 90 days.

                                 YES [X] NO [ ]


Indicate the number of shares outstanding of each of the issuer's classes of
common stock, as of the latest practicable date:

Common stock $.001 par value                            23,528,299 shares
----------------------------                         -----------------------
           Class                                 Outstanding at October 31, 2000

<PAGE>   2

                                      INDEX



<TABLE>
<CAPTION>
PART I:   FINANCIAL INFORMATION                                                           PAGE
<S>    <C>                                                                                <C>

  ITEM 1:    FINANCIAL STATEMENTS

      Consolidated Balance Sheets at September 30, 2000 (unaudited) and
      December 31, 1999                                                                     3

      Consolidated Statements of Operations for the three
      and nine months ended September 30, 2000 and 1999 (unaudited)                         4

      Consolidated Statements of Cash Flows for the nine months
      ended September 30, 2000 and 1999 (unaudited)                                         5

      Notes to Consolidated Financial Statements                                            6

  ITEM 2:   MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND
            RESULTS OF OPERATIONS                                                           7

  ITEM 3:   QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK                     10

PART II:    OTHER INFORMATION

  ITEM 1:   Legal Proceedings                                                              14

  ITEM 2:   Changes in Securities and Use of Proceeds                                      14

  ITEM 3:   Defaults Upon Senior Securities                                                15

  ITEM 4:   Submission of Matters to a Vote of Security Holders                            15

  ITEM 5:   Other Information                                                              15

  ITEM 6:   Exhibits and Reports on Form 8-K                                               15

SIGNATURES                                                                                 16
</TABLE>



                                       2
<PAGE>   3

                          PART I: FINANCIAL INFORMATION

ITEM 1: FINANCIAL STATEMENTS


                        APPLIED MOLECULAR EVOLUTION, INC.
                           CONSOLIDATED BALANCE SHEETS
                 (IN THOUSANDS, EXCEPT SHARE AND PER SHARE DATA)

<TABLE>
<CAPTION>
                                                                       SEPTEMBER 30,    DECEMBER 31,
                                                                           2000             1999
                                                                       -------------    ------------
                                                                        (UNAUDITED)
<S>                                                                    <C>              <C>
ASSETS
Current assets:
  Cash and cash equivalents                                              $  41,035       $   1,974
  Short-term investments                                                    63,694           1,524
  Prepaid expenses and other current assets                                  1,948             611
                                                                         ---------       ---------
    Total current assets                                                   106,677           4,109

Property and equipment, net                                                    620             442
Patents, net                                                                 1,521           1,344
Other assets                                                                   131              42
                                                                         ---------       ---------
    Total assets                                                         $ 108,949       $   5,937
                                                                         =========       =========

LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
  Accounts payable and accrued liabilities                               $   1,137       $     629
  Current portion of deferred revenue                                          268             237
  Current portion of long-term obligations                                      19              18
                                                                         ---------       ---------
    Total current liabilities                                                1,424             884

Deferred rent                                                                   81             114
Long-term deferred revenue                                                     690             868
Long-term obligations, less current portion                                      3              17
Minority interest                                                              134             224

Stockholders' equity:
Preferred stock, $.001 par value, 5,000,000 shares authorized,
    0 shares issued and outstanding at September 30, 2000;
    11,810,666 shares authorized, 11,640,124 shares issued and
    outstanding at December 31, 1999                                          --                12
Common stock, $.001 par value, 45,000,000 shares authorized,
    23,524,799 shares issued and outstanding at September 30, 2000;
    22,450,000 shares authorized 2,569,846 shares issued and
    outstanding at December 31, 1999                                            24               3
Additional paid-in-capital                                                 158,107          31,831
Notes receivable from employees                                               (814)           --
Deferred compensation                                                      (13,464)           (649)
Unrealized gain (loss) on short-term investments                               107              (8)
Accumulated deficit                                                        (37,343)        (27,359)
                                                                         ---------       ---------
    Total stockholders' equity                                             106,617           3,830
                                                                         ---------       ---------
    Total liabilities and stockholders' equity                           $ 108,949       $   5,937
                                                                         =========       =========
</TABLE>


                             See accompanying notes.



                                       3
<PAGE>   4

                        APPLIED MOLECULAR EVOLUTION, INC.
                      CONSOLIDATED STATEMENTS OF OPERATIONS
                      (IN THOUSANDS, EXCEPT PER SHARE DATA)
                                   (UNAUDITED)


<TABLE>
<CAPTION>
                                                                     FOR THE THREE MONTHS           FOR THE NINE MONTHS
                                                                      ENDED SEPTEMBER 30,           ENDED SEPTEMBER 30,
                                                                    -----------------------       -----------------------
                                                                      2000           1999           2000           1999
                                                                    --------       --------       --------       --------
<S>                                                                 <C>            <C>            <C>            <C>
Revenue
  Contract revenue ...........................................      $    500       $  1,436       $  1,539       $  1,783
  Other revenue ..............................................           168            139            337            257
                                                                    --------       --------       --------       --------
  Total revenue ..............................................           668          1,575          1,876          2,040
                                                                    --------       --------       --------       --------

Operating expenses
  Research and development ...................................         1,017          1,815          2,493          3,516
  General and administrative .................................           631            300          1,552            945
  Non-cash, stock based compensation .........................         3,859            209          9,293            280
                                                                    --------       --------       --------       --------
  Total operating expenses ...................................         5,507          2,324         13,338          4,741
                                                                    --------       --------       --------       --------
Loss from operations .........................................        (4,839)          (749)       (11,462)        (2,701)
Minority interest ............................................            12           --               90           --
Interest income, net .........................................         1,265             56          1,388            153
                                                                    --------       --------       --------       --------
Net loss .....................................................        (3,562)          (693)        (9,984)        (2,548)

Deemed dividend on Series F preferred stock ..................          --             --          (10,100)          --
                                                                    --------       --------       --------       --------

Net loss applicable to common stockholders ...................      $ (3,562)      $   (693)      $(20,084)      $ (2,548)
                                                                    ========       ========       ========       ========

  Basic and diluted net loss per common share
  applicable to common stockholders ..........................      $  (0.22)      $  (0.27)      $  (2.77)      $  (1.07)

  Basic and diluted net loss per common share ................      $  (0.22)      $  (0.27)      $  (1.38)      $  (1.07)

  Weighted average shares used in computing basic
  and diluted net loss per common share ......................        16,435          2,569          7,249          2,382

  Pro forma basic and diluted net loss per common share ......      $  (0.17)      $  (0.05)      $  (0.60)      $  (0.18)

  Weighted average shares used in computing basic
  and diluted pro forma net loss per common share ............        20,510         14,209         16,649         14,022
</TABLE>


                             See accompanying notes.



                                       4
<PAGE>   5

                        APPLIED MOLECULAR EVOLUTION, INC.
                      CONSOLIDATED STATEMENTS OF CASH FLOWS
                                 (IN THOUSANDS)
                                   (UNAUDITED)


<TABLE>
<CAPTION>
                                                                      NINE MONTHS ENDED
                                                                        SEPTEMBER 30,
                                                                ---------------------------
                                                                  2000              1999
                                                                ---------         ---------
<S>                                                             <C>               <C>
OPERATING ACTIVITIES
Net loss                                                        $  (9,984)        $  (2,548)
Adjustments to reconcile net loss to net cash
  used in operating activities:
  Amortization of stock-based compensation                          8,401               280
  Depreciation and amortization                                       190               179
  Realized gain of short-term investments                             (20)             --
  Compensation related to consultant stock option                     892              --
  Deferred revenue                                                   (146)             (177)
  Deferred rent                                                       (33)               (5)
  Accrued interest income                                             (15)             --
  Minority interest                                                   (90)             --
Changes in operating assets and liabilities:
  Prepaid expenses and other assets                                (1,426)             (414)
  Accounts payable and accrued expenses                               508             1,110
                                                                ---------         ---------
Net cash flows used in operating activities                        (1,723)           (1,575)
                                                                ---------         ---------

INVESTING ACTIVITIES
Purchase of property and equipment                                   (287)              (29)
Purchase of short-term investments                                (71,660)           (3,684)
Proceeds from sale of short-term investments                        9,625             1,684
Patents                                                              (258)             (179)
                                                                ---------         ---------
Net cash flows used in investing activities                       (62,580)           (2,208)
                                                                ---------         ---------

FINANCING ACTIVITIES
Payments on long-term obligation                                      (13)              (22)
Issuance of common stock, net                                      93,365             5,110
Issuance of preferred stock, net                                   10,012              --
                                                                ---------         ---------
Net cash flows provided by financing activities                   103,364             5,088
                                                                ---------         ---------

Net increase in cash and cash equivalents                          39,061             1,305
Cash and cash equivalents at the beginning of the period            1,974               824
                                                                ---------         ---------

Cash and cash equivalents at the end of the period              $  41,035         $   2,129
                                                                =========         =========
</TABLE>


                             See accompanying notes.



                                       5
<PAGE>   6

                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                  (UNAUDITED)

1.  Organization and Business

    Applied Molecular Evolution, Inc., or the Company or AME, a Delaware
    corporation, was incorporated on August 14, 1989, as Ixsys, Inc., and
    changed its name to Applied Molecular Evolution, Inc. in February 2000. The
    Company has a broad technology platform termed AMEsystem(TM), which the
    Company's management believes will provide AME with a valuable and efficient
    solution to optimizing proteins with commercial potential. To date, the
    Company has successfully utilized its proprietary technology to optimize
    monoclonal antibodies for pharmaceutical and biotechnology companies.

2.  Basis of Presentation

    The accompanying unaudited consolidated financial statements have been
    prepared by the Company in accordance with generally accepted accounting
    principles for interim financial information. Accordingly, they do not
    include all the information and footnotes required by generally accepted
    accounting principles for complete financial statements. In the opinion of
    management, all adjustments, consisting of normal recurring accruals, which
    are necessary for a fair statement of the results of the interim periods
    presented, have been included. The results of operations for the interim
    period are not necessarily indicative of results to be expected for any
    other interim period or for the year as a whole. These unaudited
    consolidated financial statements and footnotes thereto should be read in
    conjunction with the audited financial statements and footnotes thereto
    contained in the Company's Registration Statement on Form S-1 filed with the
    Securities and Exchange Commission, or the SEC, in the form in which it
    became effective on July 27, 2000.

    The preparation of financial statements in accordance with generally
    accepted accounting principles requires management to make estimates and
    assumptions that affect amounts reported in the consolidated financial
    statements and related footnotes. Changes in the estimates may affect
    amounts reported in future periods.

    The consolidated financial statements include the accounts of the Company
    and Novasite Pharmaceuticals, Inc., or Novasite, which is 78% owned by AME
    and which was incorporated in July 1999. All significant intercompany
    accounts and transactions have been eliminated.

3.  Initial Public Offering of Common Stock

    On July 27, 2000, the Company completed its initial public offering of
    5,347,500 shares of common stock at $19.00 per share, including 697,500
    shares of common stock issued pursuant to the underwriters' over-allotment
    option. The combined gross proceeds raised by the Company from the offering
    and over-allotment option were $101.6 million. Concurrent with the initial
    public offering, 13,884,568 shares of convertible preferred stock were
    converted to shares of common stock.

4.  Computation of Net Loss Per Share

    Basic and diluted net loss per common share are presented in conformity with
    Statement of Financial Accounting Standards No. 128 "Earnings per Share"
    (SFAS No. 128) and Staff Accounting Bulletin 98 issued by the Staff of the
    Securities and Exchange Commission (SAB 98), for all periods presented.
    Under the provisions of SAB 98, common and preferred stock that has been
    issued or granted for nominal consideration prior to the anticipated
    effective date of the initial public offering must be included in the
    calculation of basic and diluted net loss per common share as if these
    shares had been outstanding for all periods presented. To date, the Company
    has not issued or granted shares for nominal consideration. In accordance
    with SFAS No. 128, basic and diluted net loss per share has been computed
    using the weighted average number of shares of common stock outstanding
    during the period, less shares subject to repurchase. Pro forma basic and
    diluted net



                                       6
<PAGE>   7

    loss per common share, as presented in the statements of operations, has
    been computed for the three and nine months ended September 30, 2000 and
    1999, as described above, and also gives effect to the assumed conversion of
    preferred stock which automatically converted to common stock upon the
    completion of the Company's initial public offering (using the "as if
    converted" method) from the original date of issuance.

5.  Recently Issued Accounting Pronouncements

    In June 1998, the Financial Accounting Standards Board issued SFAS No.
    133 "Accounting for Derivative Instruments and Hedging Activities", which
    will be effective for our fiscal year 2001. SFAS 133 establishes accounting
    and reporting standards requiring that every derivative instrument,
    including certain derivative instruments embedded in other contracts, be
    recorded in the balance sheet as either an asset or liability measured at
    its fair value. SFAS 133 also requires that changes in the derivative's fair
    value be recognized in earnings unless specific hedge accounting criteria
    are met. We believe that adoption of SFAS 133 will not have a material
    effect on our financial statements, since we currently do not hold
    derivative instruments or engage in hedging activities.


ITEM 2: MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
OF OPERATIONS

The statements in this quarterly report that are not descriptions of historical
facts may be forward-looking statements that are subject to risks and
uncertainties. Actual results could differ materially from those currently
anticipated due to a number of factors, including those identified below and in
our other publicly available documents. We are under no obligation to update any
of these forward-looking statements after the filing of this quarterly report to
reflect actual results or changes in our expectations.

The following information should be read in conjunction with the consolidated
financial statements and the notes thereto included in Item 1 of this quarterly
report. We also urge readers to review and consider our disclosures describing
various factors that affect our business, including the disclosures under
Management's Discussion and Analysis of Financial Condition and Results of
Operations and Risk Factors and the audited financial statements and notes
thereto contained in our Registration Statement on Form S-1, filed with the SEC
in the form in which it became effective on July 27, 2000.

OVERVIEW

We are a leader in the application of directed evolution to the development of
biotherapeutics. Directed evolution is the process by which genes and proteins
are optimized for specific commercial purposes. We focus principally on applying
our technology to human biotherapeutics, the largest and most profitable target
market for directed evolution.

Since our formation, we have expended considerable resources on the development
of our AMEsystem technology and the development of Vitaxin, a product candidate
engineered from an antibody we licensed from The Scripps Research Institute.
Much of our research and development from 1995-1999 was allocated to preclinical
development and initial clinical trials for Vitaxin. In 1999 we licensed Vitaxin
to MedImmune, which is responsible for future clinical development expenses and
commercialization. MedImmune is preparing to initiate clinical trials with an
improved, second generation version of Vitaxin that we enhanced using our
AMEsystem technology.

To date we have generated revenue from research collaborations, product and
technology licenses, prepaid royalties and government grants. We have strategic
collaborations with MedImmune, Bristol-Myers Squibb, and Cell Matrix. We have
licensed intellectual property to Biosite Diagnostics, Inc. in exchange for a
non-refundable, prepaid, fixed royalty which is being recognized over six years,
the estimated useful lives of the related patents. Our government grants have
come from the National Institutes of Health. Research funding from corporate
collaborators and government grants is recognized as revenue when the services
are rendered.



                                       7
<PAGE>   8

We have incurred losses since our inception. As of September 30, 2000, we had an
accumulated deficit of $37.3 million. These losses and this accumulated deficit
resulted from the significant costs incurred in the development of our
technology platform and the clinical development of Vitaxin. We expect these
losses to increase as we continue to invest in our AMEsystem technology and
internal development projects.

We have capitalized the costs incurred to file patent applications. These costs
are amortized over a six-year estimated life from the date of patent issuance.
At September 30, 2000, we had capitalized costs related to issued patents
totaling approximately $402,000 (net of accumulated amortization) and
approximately $1.1 million related to unissued patents. Our results of
operations could be materially impacted when we begin amortizing the costs
related to unissued patents. In addition, we expense all costs related to
abandoned patent applications. If we elect to abandon any of our currently
issued or unissued patents, the related expense could be material to our results
of operations for the period of the abandonment.

RESULTS OF OPERATIONS

Three Months Ended September 30, 2000 and 1999

Revenue. Our revenue decreased to $668,000 for the quarter ended September 30,
2000 from $1.6 million for the same period in 1999, a decrease of approximately
$900,000. The decrease was primarily due to the one time Vitaxin licensing
revenue of $1.2 million received from MedImmune in the quarter ended September
30, 1999.

Research and development. Research and development expenses decreased to $1.0
million for the quarter ended September 30, 2000 from $1.8 million for the same
period in 1999, a decrease of approximately $800,000. The decrease was related
primarily to the elimination of clinical costs and staffing related to the
Vitaxin project which were incurred in the third quarter of 1999 and were not
incurred in the third quarter of 2000 as Vitaxin was licensed to MedImmune in
1999.

General and administrative. General and administrative expenses increased to
$631,000 for the quarter ended September 30, 2000 from $300,000 for the same
period in 1999, an increase of $331,000. The increase was due primarily to the
expansion of the administrative infrastructure to support the needs of a public
company and an increase in professional fees in connection with the expansion of
our business development efforts.

Stock-based compensation. Deferred compensation for options granted to employees
is the difference between the exercise price and the estimated fair value of our
common stock on the date the options were granted. Deferred compensation is
included as a component of stockholders' equity and is being amortized in
accordance with FASB Interpretation No. 28 over the vesting periods of the
related options, which is generally four years.

Deferred compensation for options granted to consultants has been determined in
accordance with the Statement of Financial Accounting Standards No. 123,
"Accounting for Stock - Based Compensation", as the fair value of the equity
instruments issued, and is periodically remeasured as the underlying options
vest in accordance with EITF 96-18.

For the three months ended September 30, 2000, we recorded non-cash, stock-based
compensation expenses of approximately $3.9 million ($1.1 million and $2.8
million related to research and development and general and administrative,
respectively), compared to $209,000 for the same period in 1999.

Interest income, net. Net interest income increased to $1.3 million for the
quarter ended September 30, 2000 from $56,000 for the quarter ended September
30, 1999, an increase of $1.2 million. The increase was due primarily to our
higher average cash and investment balances during 2000 as a result of the cash
proceeds from the initial public offering which closed in the third quarter of
2000.

Nine Months Ended September 30, 2000 and 1999



                                       8
<PAGE>   9

Revenue. Our revenue decreased to $1.9 million for the nine months ended
September 30, 2000 from $2.0 million for the same period in 1999, a decrease of
$100,000. Revenue from collaborations accounted for 82% and 87% of all revenue
for the nine months ended September 30, 2000 and 1999, respectively.

Research and development. Research and development expenses decreased to $2.5
million for the nine months ended September 30, 2000 from $3.5 million for the
same period in 1999, a decrease of approximately $1.0 million. The decrease was
related primarily to the elimination of clinical costs and staffing related to
the Vitaxin project which were incurred in 1999 and were not incurred in 2000 as
Vitaxin was licensed to MedImmune in 1999.

General and administrative. General and administrative expenses increased to
$1.6 million for the nine months ended September 30, 2000 from $945,000 for the
same period in 1999, an increase of approximately $655,000. The increase was due
primarily to the expansion of the administrative infrastructure to support the
needs of a public company and professional fees in connection with the expansion
of our business development efforts.

Stock-based compensation. For the nine months ended September 30, 2000, we
recorded non-cash, stock-based compensation expenses of approximately $9.3
million ($3.0 million and $6.3 million related to research and development and
general and administrative, respectively), compared to $280,000 for the same
period in 1999.

Deemed dividend on beneficial conversion of Series F preferred stock. On May 3,
2000 and June 15, 2000, we issued 1,133,333 shares and 1,111,111 shares of our
Series F preferred stock for $5.1 million and $5.0 million, respectively, which
converted into shares of common stock upon the closing of our initial public
offering. We recorded a charge of $10.1 million to earnings applicable to common
stockholders for the beneficial conversion feature embedded in the Series F
preferred stock.

Interest income, net. Net interest income increased to $1.4 million for the nine
months ended September 30, 2000 from $153,000 for the same period in 1999, an
increase of approximately $1.2 million. The increase was due primarily to our
higher average cash and investment balances during 2000 as a result of the cash
proceeds from the initial public offering which closed in the third quarter of
2000.


LIQUIDITY AND CAPITAL RESOURCES


In July 2000, we sold 5.3 million shares of Common Stock in an initial public
offering resulting in net proceeds to the Company of approximately $94.5 million
(excluding offering expenses). Prior to the initial public offering, we had
financed our operations primarily through private placements of equity
securities, with aggregate net proceeds of approximately $39.9 million. In
addition, we have generated $17.1 million of cash from research collaborations
through September 30, 2000.

As of September 30, 2000, we had approximately $105 million in cash, cash
equivalents and short-term investments, compared to $3.5 million of cash, cash
equivalents and short-term investments as of December 31, 1999.

For the nine months ended September 30, 2000, we used cash of approximately $1.7
million in operating activities to fund our net losses of $10.0 million, offset
by non-cash charges for depreciation and patent amortization totaling $190,000,
non-cash, stock based compensation totaling $9.3 million and decreases in
deferred revenue of $146,000.

For the nine months ended September 30, 2000, we used cash of approximately
$62.6 million in investing activities. Our investing activities consisted
primarily of purchases and sales of short-term investments, and capital
expenditures for property and equipment to be used in our business. We expect to
continue to make investments in our infrastructure, including purchasing
property and equipment to support our operations.

For the nine months ended September 30, 2000, we generated $103.4 million of
cash from financing activities, primarily from the net proceeds of the initial
public offering and the sale of Series F preferred stock.



                                       9
<PAGE>   10

We expect our cash requirements to increase significantly in 2000 as we continue
our research and development efforts, hire additional personnel, grow our
administrative support activities and expand our facilities. We believe that our
current cash, cash equivalents and short-term investments will be sufficient to
fund our operations for three years.

This estimate is a forward-looking statement that involves risks and
uncertainties. Our future capital requirements depend on several factors,
including: the success of our research and development efforts; our ability to
establish collaborative agreements; our costs of prosecuting and maintaining
patents; and market and competing technological developments.

Our plans include the development of selected internal projects to a point where
they may be candidates for corporate collaborations. If we choose to develop and
commercialize any internal development projects without the assistance of
collaborators, the costs of development and commercialization would exceed our
capital resources. We would therefore need to seek additional sources of
financing to further develop these projects ourselves.

Should we require additional financing due to unanticipated developments, such
financing may not be available when needed or may not be available on favorable
terms. We may either delay, scale back or eliminate some or all of our research
and development programs for lack of funds. Furthermore, our ability to operate
as a going concern may be adversely affected by insufficient funds. If
additional funds are raised by issuing equity securities, substantial dilution
to existing stockholders my result.

ITEM 3: QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

The primary objective of our investment activities is to preserve principal
while at the same time maximizing the income we receive from our investments
without significantly increasing risk. Some of the securities that we invest in
may have market risk. This means that a change in prevailing interest rates may
cause the principal amount of the investment to fluctuate. For example, if we
hold a security that was issued with a fixed interest rate at the
then-prevailing rate and the prevailing interest rate later rises, the market
value of our investment will probably decline. To minimize this risk in the
future, we intend to maintain our portfolio of cash equivalents and short-term
investments in a variety of securities, including commercial paper, money market
funds, and government and non government debt securities. The average duration
of all of our investments in 2000 was less than one year. Due to the short-term
nature of these investments, we believe that we have no material exposure to
interest rates arising from our investments. Therefore, no quantitative tabular
disclosure is included in this report.

                                  RISK FACTORS

WE HAVE NOT ACHIEVED PROFITABILITY AND MAY NEVER BECOME PROFITABLE.

We are at an early stage of development. We incurred a net loss of $10.0 million
for the nine months ended September 30, 2000, and our revenue for that same
period was only $1.9 million. Additionally, we have had net losses each year
since inception and, as of September 30, 2000, had an accumulated deficit of
$37.3 million. We expect to report a net loss for fiscal year 2000, and we
expect to report increasing net losses for the foreseeable future. We may never
achieve profitability. The size of our net losses will depend, in part, on the
rate of growth, if any, in our contract revenue and on the level of our
expenses. To date, we have derived most of our revenue from collaborations and
expect to continue to do so in the foreseeable future. Revenues from
collaborations are uncertain because our ability to secure future agreements
will depend upon our ability to address the needs of our potential
collaborators. We expect to spend significant amounts to fund research and
development and enhance our core technology. We expect that our operating
expenses will increase significantly in the near term, and consequently, we will
need to generate significant additional revenue to achieve profitability. Even
if we do achieve profitability, we may not be able to sustain or increase
profitability on a quarterly or annual basis.



                                       10
<PAGE>   11

WE MAY NEED ADDITIONAL CAPITAL IN THE FUTURE. IF ADDITIONAL CAPITAL IS NOT
AVAILABLE, WE MAY HAVE TO CURTAIL OR CEASE OPERATIONS.

We may need to raise more money to continue our operations. We may seek
additional funds from public and private stock offerings, corporate
collaborations, borrowings under lease lines of credit or other sources. If we
cannot raise more money, we may have to reduce our capital expenditures, scale
back our development of new products, reduce our workforce or license to others
products that we otherwise would seek to commercialize ourselves. We expect that
our current resources, together with future operating revenue, will be
sufficient to fund operations for the next three years. The amount of money we
will need will depend on many factors, including:

     -  the success of our research and development efforts

     -  our ability to establish collaborative agreements

     -  our costs of prosecuting and maintaining patents

     -  market and competing technological developments

Additional capital may not be available on terms acceptable to us, or at all.
Any additional equity financing may be dilutive to stockholders, and debt
financing, if available, may include restrictive covenants.

THE COMMERCIAL UTILITY OF OUR AMEsystem TECHNOLOGY IS UNPROVEN AND MAY NEVER BE
REALIZED.

While we have met with initial success in applying our AMEsystem technology, to
prove the commercial value of our technology, we or our collaborators will need
to commercialize biotherapeutics that we have optimized. Successful
commercialization of biotherapeutics requires: preclinical testing, clinical
trials, regulatory approval and commercial manufacturing. It will take us or our
collaborators many years to complete these steps for any biotherapeutic. If we
or our collaborators do not undertake and successfully complete these
activities, then our AMEsystem technology will be of little commercial value,
and our ability to generate revenue will be limited. Currently, there are no
products in clinical trials that have been developed using our technology.

WE HAVE OPTIMIZED ONLY ONE TYPE OF PROTEIN AND MAY NOT BE ABLE TO OPTIMIZE
OTHERS, THEREBY LIMITING OUR MARKET POTENTIAL.

To date we have optimized only antibodies for corporate collaborators. If we are
unable to apply our AMEsystem technology to other types of proteins, the scope
of our potential business will be significantly limited.

IF OUR COLLABORATORS ARE NOT SUCCESSFUL OR IF WE ARE UNABLE TO FIND
COLLABORATORS IN THE FUTURE, WE MAY NOT BE ABLE TO COMMERCIALIZE PRODUCT
CANDIDATES.

Our strategy for developing and commercializing product candidates calls for us
to enter into contractual arrangements with collaborators. We may be
unsuccessful in attracting collaborators to develop and commercialize our
products. Some collaborators may not perform their obligations as we expect, or
we may not derive any revenue from these arrangements. We do not know whether
these collaborators will



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<PAGE>   12

successfully develop and market any products under their respective agreements.
Moreover, some of our collaborators are also researching competing technologies
and products targeted by our collaborative programs. Our success depends in part
upon the performance by these collaborators of their responsibilities under
these arrangements. We have no control over the resources that any collaborator
may devote to the development and commercialization of products under these
collaborations. Our collaborators may terminate their agreements with us or
otherwise fail to conduct their collaborative activities successfully and in a
timely manner. Our collaborators may elect not to develop products arising out
of our collaborative arrangements or not to devote sufficient resources to
develop, manufacture, market or sell these products.

IF PRODUCT CANDIDATES WE OPTIMIZE DO NOT RECEIVE REGULATORY APPROVAL, NEITHER WE
NOR OUR COLLABORATORS WILL BE ABLE TO COMMERCIALIZE THESE PRODUCTS.

The U.S. Food and Drug Administration, or FDA, must approve any therapeutic
product before it can be marketed in the United States. The regulatory process
is expensive and time-consuming. Before we or a collaborator can file a new drug
application with the FDA, the product candidate must undergo extensive testing,
including animal studies and human clinical trials that can take many years and
may require substantial expenditures. Data obtained from such testing may be
susceptible to varying interpretations which could delay, limit or prevent
regulatory approval. Changes in regulatory policy for product approval may cause
delays or rejections. Because our product candidates will be developed in a
novel way, government regulatory authorities may subject these product
candidates to greater scrutiny than those developed using more conventional
methods. Some of our collaborators are in early stages of the FDA regulatory
process for drugs we have optimized.

IF WE ARE UNABLE TO ADEQUATELY PROTECT OUR PROPRIETARY TECHNOLOGY, OUR
COMPETITIVE POSITION COULD BE HURT.

The patent positions of biopharmaceutical and biotechnology companies, including
our patent position, are generally uncertain and involve complex legal and
factual questions. We may be able to protect our proprietary rights from
infringement by third parties only to the extent that our proprietary
technologies are covered by valid and enforceable patents or are effectively
maintained as trade secrets. Furthermore, others may independently develop
similar or alternative technologies or design around our patented technologies.
Litigation or other proceedings to defend or enforce our intellectual property
rights could require us to spend significant time and money and could disrupt
and harm our business.

We also rely upon trade secrets, technical know-how and continuing inventions to
develop and maintain our competitive position. Others may independently develop
substantially equivalent proprietary information and techniques or otherwise
gain access to our trade secrets or disclose our technology, and we may not be
able to meaningfully protect our trade secrets or be capable of protecting our
rights to our trade secrets.

IF WE INFRINGE THIRD-PARTY PATENTS OR BREACH OUR LICENSE AGREEMENTS, LITIGATION
MAY DEPLETE OUR RESOURCES AND UNDERMINE OUR ABILITY TO USE OUR AMEsystem
TECHNOLOGY.

Our commercial success also depends in part on neither infringing valid,
enforceable patents or proprietary rights of third parties, nor breaching any
licenses that may relate to our technology and products. We are aware of
third-party patents that may relate to our technology. It is possible that we
may unintentionally infringe these patents or other patents or proprietary
rights of third parties. Any legal action taken against us or our collaborative
partners claiming damages and seeking to enjoin commercial



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<PAGE>   13

activities relating to our products and processes affected by third-party rights
may require us or our collaborators to obtain licenses in order to continue to
manufacture or market the affected products and processes. In addition, these
actions may subject us to potential liability for damages. We or our
collaborators may not prevail in an action, and any license required under a
patent may not be made available on commercially acceptable terms, or at all.
Litigation could result in substantial costs and the diversion of management's
efforts, regardless of the result of the litigation.

IF WE LOSE OUR KEY PERSONNEL OR ARE UNABLE TO ATTRACT AND RETAIN ADDITIONAL
PERSONNEL, WE MAY BE UNABLE TO SUCCESSFULLY DEVELOP OUR TECHNOLOGY.

We are highly dependent on the principal members of our management and
scientific staff, particularly our President and Chief Executive Officer,
William D. Huse, M.D., Ph.D. If we lose their services we may not achieve our
objectives. In addition, recruiting and retaining qualified scientific personnel
to perform future research and development work will be critical to our success.
We do not have sufficient personnel to fully execute our business plan, and
there is currently a shortage of skilled executives and scientists, which is
likely to continue. As a result, competition for experienced executives and
scientists from numerous companies and academic and other research institutions
may limit our ability to hire or retain personnel on acceptable terms. If we
fail to attract and retain sufficient personnel, we may not be able to develop
or implement our technology.

PUBLIC PERCEPTION OF ETHICAL AND SOCIAL ISSUES MAY LIMIT THE USE OF OUR
TECHNOLOGY, WHICH COULD REDUCE OUR REVENUE.

Our success will depend upon our ability to develop products through the
application of our directed evolution technology. Governmental authorities
could, for social or other purposes, limit the use of genetic modification or
prohibit the practice of our technology. Ethical and other concerns about the
use of products derived from modified genes could adversely affect their market
acceptance. If, as a result, our technology or the products we develop cannot be
marketed, we would lose our core business.

WE USE HAZARDOUS CHEMICALS AND RADIOACTIVE AND BIOLOGICAL MATERIALS IN OUR
BUSINESS. ANY CLAIMS RELATING TO IMPROPER HANDLING, STORAGE OR DISPOSAL OF THESE
MATERIALS COULD BE TIME-CONSUMING AND COSTLY.

We use hazardous materials, including chemicals, and radioactive and biological
materials. These materials include o-phenylenediamine dihydrochloride, ethidium
bromide, and acrylamide. Our operations also produce hazardous waste products.
We cannot eliminate the risk of accidental contamination or discharge and any
resultant injury from these materials. We could be subject to civil damages in
the event of an improper or unauthorized release of, or exposure of individuals
to, hazardous materials. In addition, claimants may sue us for injury or
contamination that results from the use of these materials. Federal, state and
local laws and regulations govern the use, manufacture, storage, handling and
disposal of these materials. Compliance with environmental laws and regulations
may be expensive, and current or future environmental regulations may impair our
research, development, or production efforts.

IF PEOPLE ARE HARMED BY DRUGS DEVELOPED USING OUR AMEsystem TECHNOLOGY, WE MAY
BE SUED FOR PRODUCT LIABILITY.

We may be sued for product liability and other claims if our technology or
products developed from our technology are alleged to have caused harm. We may
not be able to avoid significant liability exposure.



                                       13
<PAGE>   14

We maintain product liability insurance, but we may not have sufficient
coverage. If we are sued for any injury caused by our products and found liable,
our financial condition, reputation and ability to find collaborators may be
harmed.

SUBSTANTIAL SALES OF OUR COMMON STOCK BY OUR EXISTING STOCKHOLDERS COULD CAUSE
OUR STOCK PRICE TO FALL.

Future sales of common stock by our stockholders under Rule 144 of the
Securities Act of 1933, or the Securities Act, or through the exercise of
outstanding registration rights or otherwise could have an adverse effect on the
price of our common stock. Some of our existing stockholders have rights to
require us to register their shares for future sale.

OUR OFFICERS AND DIRECTORS AND THEIR AFFILIATES OWN SLIGHTLY LESS THAN A
MAJORITY OF OUR SHARES AND MAY VOTE IN WAYS WITH WHICH YOU DISAGREE BECAUSE THEY
HAVE INTERESTS BOTH AS MANAGERS AND STOCKHOLDERS.

As of September 30, 2000, our officers and directors and their affiliates, in
the aggregate, own beneficially approximately 39.7% of our outstanding shares of
common stock. As a result, these stockholders, acting together, would be able to
effectively control most matters requiring approval by our stockholders,
including the election of a majority of the directors. If your interests as a
stockholder are different from their interests as both managers and
stockholders, you may not agree with their decisions.


                           PART II: OTHER INFORMATION

ITEM 1:        LEGAL PROCEEDINGS

               None.

ITEM 2:        CHANGES IN SECURITIES AND USE OF PROCEEDS

        (a)    Not applicable.

        (b)    Not applicable.

        (c)    On various dates from July 1, 2000 through September 30, 2000,
               the Company issued 335,985 shares of its common stock to various
               employees and consultants pursuant to the exercise of options
               granted under its 1992 Stock Plan or 2000 Stock Plan. The
               exercise price per share ranged from $0.04 to $1.25. The Company
               relied on the exemption provided by Rule 701 promulgated under
               the Securities Act in issuing these shares.

        (d)    On July 27, 2000 the Company sold 5,347,500 shares of its common
               stock priced at $19.00 per share for an aggregate offering price
               of $101.6 million in an initial public offering, or IPO, led by
               an underwriting group consisting of CIBC World Markets,
               PaineWebber Incorporated and SG Cowen. The proceeds of the IPO to
               the Company, net of underwriting fees, were $94.5 million. IPO
               expenses were approximately $1.6 million. The effective date of
               the registration statement filed by the company with the
               Securities and Exchange Commission in connection with the IPO
               (File No. 333-36830) was July 27, 2000. From July 27, 2000 to
               September 30, 2000, we invested the net



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<PAGE>   15

               proceeds from the offering in cash equivalents and short-term
               investments.


ITEM 3:        DEFAULTS UPON SENIOR SECURITIES

               Not applicable.

ITEM 4:        SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

               None.

ITEM 5:        OTHER INFORMATION

               Not Applicable.

ITEM 6:        EXHIBITS AND REPORTS ON FORM 8-K

     (a) Exhibits

               27.1  Financial Data Schedule

     (b) Reports on Form 8-K during the first quarter

               None.



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<PAGE>   16

                                   SIGNATURES

Pursuant to the requirements of the Securities and Exchange Act of 1934, the
registrant has duly caused this report to be signed on its behalf by the
undersigned thereunto duly authorized.





Date:    November 9, 2000           By: /s/ WILLIAM D. HUSE
     ------------------------           ----------------------------------------
                                        William D. Huse, M.D., Ph.D., President
                                        and Chief Executive Officer


Date:    November 9, 2000           By: /s/ LAWRENCE E. BLOCH
     ------------------------           ----------------------------------------
                                        Lawrence E. Bloch, M.D., Chief Financial
                                        Officer, Vice President of Business
                                        Development and Secretary



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