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<TITLE>Applied Molecular Evolution, Inc. Form S-8</TITLE>
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<H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>

<P align="center"><FONT size="2">As filed with the Securities and Exchange Commission on November&nbsp;16, 2001
</FONT>

<P align="right"><FONT size="2">Registration No.&nbsp;333-
</FONT>

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<P align="center"><FONT size="2"><B>SECURITIES AND EXCHANGE COMMISSION<BR>
Washington, D.C. 20549</B>
</FONT>

<P align="center"><FONT size="5"><B>Form&nbsp;S-8</B>
</FONT>

<P align="center"><FONT size="2"><B>REGISTRATION STATEMENT<BR>
Under<BR>
THE SECURITIES ACT OF 1933</B>
</FONT>

<DIV align="center"><FONT size="2">&nbsp;
</FONT></DIV>
<DIV align="center"><FONT size="4"><B>Applied Molecular Evolution, Inc.</B>
</FONT></DIV>
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<DIV align="center"><FONT size="2">(Exact name of registrant as specified in its charter)
</FONT></DIV>
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        <TD width="45%">&nbsp;</TD>
        <TD width="10%">&nbsp;</TD>
        <TD width="45%">&nbsp;</TD>
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<TR valign="bottom">
        <TD align="center" valign="top"><FONT size="2"><B>Delaware</B></FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="center" valign="top"><FONT size="2">
<B>33-0374014</B></FONT></TD>
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        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="center" valign="top"><FONT size="2">
<HR size="1" noshade></FONT></TD>
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        <TD align="center" valign="top"><FONT size="2">(State or other jurisdiction of<BR>
incorporation or organization)</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="center" valign="top"><FONT size="2">
(I.R.S. Employer Identification No.)</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="bottom">
        <TD align="center" valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="center" valign="top"><FONT size="2">&nbsp;</FONT></TD>
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<TR><TD><TR><TD><TR><TD><TR><TD>
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        <TD align="center" valign="top"><FONT size="2"><B>3520 Dunhill Street<BR>
San Diego, California</B></FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="center" valign="top"><FONT size="2">&nbsp;<br>
<B>92121</B></FONT></TD>
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        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="center" valign="top"><FONT size="2">
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<TR valign="bottom">
        <TD align="center" valign="top"><FONT size="2">(Address of Principal Executive Offices)</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="center" valign="top"><FONT size="2">
(Zip Code)</FONT></TD>
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<DIV align="center"><FONT size="2">&nbsp;
</FONT></DIV>
<DIV align="center"><FONT size="2"><B>2001 STOCK INCENTIVE PLAN</B>
</FONT></DIV>
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<DIV align="center"><FONT size="2">(Full title of the plans)
</FONT></DIV>
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        <TD width="45%">&nbsp;</TD>
        <TD width="10%">&nbsp;</TD>
        <TD width="45%">&nbsp;</TD>
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        <TD align="center" valign="top"><FONT size="2">WILLIAM D. HUSE<BR>
President and Chief Executive Officer</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="center" valign="top"><FONT size="2">
Copy to:</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
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        <TD align="center" valign="top"><FONT size="2">3520 Dunhill Street<BR>
San Diego, CA 92121<BR>
(858)&nbsp;597-4990<BR>
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(Name, address and telephone number,<BR>
including area code, of agent for service)</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="center" valign="top"><FONT size="2">
THOMAS E. SPARKS, JR.<BR>
Pillsbury Winthrop LLP<BR>
50 Fremont Street<BR>
San Francisco, CA 94120-7880<BR>
(415)&nbsp;983-1000<BR>
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<TABLE cellspacing="0" border="0" cellpadding="0" width="100%">
<TR valign="bottom">
        <TD width="37%">&nbsp;</TD>
        <TD width="3%">&nbsp;</TD>
        <TD width="11%">&nbsp;</TD>
        <TD width="1%">&nbsp;</TD>
        <TD width="11%">&nbsp;</TD>
        <TD width="3%">&nbsp;</TD>
        <TD width="1%">&nbsp;</TD>
        <TD width="1%">&nbsp;</TD>
        <TD width="2%">&nbsp;</TD>
        <TD width="3%">&nbsp;</TD>
        <TD width="7%">&nbsp;</TD>
        <TD width="1%">&nbsp;</TD>
        <TD width="7%">&nbsp;</TD>
        <TD width="3%">&nbsp;</TD>
        <TD width="4%">&nbsp;</TD>
        <TD width="1%">&nbsp;</TD>
        <TD width="4%">&nbsp;</TD>
</TR>
<TR valign="bottom">
        <TD nowrap align="center" colspan="17"><FONT size="2"><B>CALCULATION OF REGISTRATION FEE</B></FONT></TD>
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<TR valign="bottom">
        <TD colspan="17"><HR size="1" noshade></TD>
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<TR valign="bottom">
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center" colspan="3"><FONT size="1"><B>Proposed</B></FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
</TR>
<TR valign="bottom">
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center" colspan="3"><FONT size="1"><B>Maximum</B></FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center" colspan="3"><FONT size="1"><B>Proposed Maximum</B></FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center" colspan="3"><FONT size="1"><B>Amount of</B></FONT></TD>
</TR>
<TR valign="bottom">
        <TD nowrap align="center"><FONT size="1"><B>Title of Securities to</B></FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center" colspan="3"><FONT size="1"><B>Amount to be</B></FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center" colspan="3"><FONT size="1"><B>Offering Price per</B></FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center" colspan="3"><FONT size="1"><B>Aggregate Offering</B></FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center" colspan="3"><FONT size="1"><B>Registration</B></FONT></TD>
</TR>
<TR valign="bottom">
        <TD nowrap align="center"><FONT size="1"><B>be Registered</B></FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center" colspan="3"><FONT size="1"><B>Registered(1)</B></FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center" colspan="3"><FONT size="1"><B>Share(2)</B></FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center" colspan="3"><FONT size="1"><B>Price(2)</B></FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center" colspan="3"><FONT size="1"><B>Fee</B></FONT></TD>
</TR>
<TR>
        <TD colspan="17" align="left"><DIV style="margin-left:10px; text-indent:-10px"><HR size="1" noshade></DIV></TD>
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<TR valign="bottom">
        <TD><DIV style="margin-left:10px; text-indent:-10px"><FONT size="2">Common Stock, par value $0.001</FONT></DIV></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD colspan="3" align="center"><FONT size="2">500,000&nbsp;shares</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="right"><FONT size="2">$</FONT></TD>
        <TD align="right"><FONT size="2">8.95</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="right"><FONT size="2">$</FONT></TD>
        <TD align="right"><FONT size="2">4,475,000.00</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="right"><FONT size="2">$</FONT></TD>
        <TD align="right"><FONT size="2">1,118.75</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
</TR>
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        <TD colspan="17" align="left"><DIV style="margin-left:10px; text-indent:-10px"><HR size="1" noshade></DIV></TD>
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      <TD width="1%" align="left" nowrap><FONT size="2">(1)</FONT></TD>
        <TD width="3%"><FONT size="2">&nbsp;</FONT></TD>
        <TD width="96%"><FONT size="2">Pursuant to Rule&nbsp;416(a) under the Securities Act, this registration
statement also includes an indeterminate number of additional shares which may
be offered and issued in connection with any stock splits, stock dividends or
similar transactions.</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="top">
      <TD width="1%" align="left" nowrap><FONT size="2">(2)</FONT></TD>
        <TD width="3%"><FONT size="2">&nbsp;</FONT></TD>
        <TD width="96%"><FONT size="2">Estimated solely for the purpose of calculating the registration fee
pursuant to Rule&nbsp;457, based upon the average of the high and low prices as
reported on the Nasdaq National Market on November&nbsp;12, 2001.</FONT></TD>
</TR>
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<P>


<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The Registration Statement shall become effective upon filing in
accordance with Rule&nbsp;462 under the Securities Act of 1933.
</FONT>
<P>
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<A name="toc"><DIV align="CENTER" style="page-break-before:always"><U><B>TABLE OF CONTENTS</B></U></DIV></A>

<P><CENTER>
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<TR><TD colspan="9"><A HREF="#000">PART I INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS</A></TD></TR>
<TR><TD></TD><TD colspan="8"><A HREF="#001">Item&nbsp;1. Plan Information</A></TD></TR>
<TR><TD></TD><TD colspan="8"><A HREF="#002">Item&nbsp;2. Registrant Information and Employee Plan Annual Information</A></TD></TR>
<TR><TD colspan="9"><A HREF="#003">PART II INFORMATION REQUIRED IN THE REGISTRATION STATEMENT</A></TD></TR>
<TR><TD></TD><TD colspan="8"><A HREF="#004">Item&nbsp;3. Incorporation of Certain Documents by Reference</A></TD></TR>
<TR><TD></TD><TD colspan="8"><A HREF="#005">Item&nbsp;4. Description of Securities</A></TD></TR>
<TR><TD></TD><TD colspan="8"><A HREF="#006">Item&nbsp;5. Interests of Named Experts and Counsel</A></TD></TR>
<TR><TD></TD><TD colspan="8"><A HREF="#007">Item&nbsp;6. Indemnification of Directors and Officers</A></TD></TR>
<TR><TD></TD><TD colspan="8"><A HREF="#008">Item&nbsp;7. Exemption from Registration Claimed</A></TD></TR>
<TR><TD></TD><TD colspan="8"><A HREF="#009">Item&nbsp;8. Exhibits</A></TD></TR>
<TR><TD></TD><TD colspan="8"><A HREF="#010">Item&nbsp;9. Undertakings</A></TD></TR>
<TR><TD colspan="9"><A HREF="#011">SIGNATURES</A></TD></TR>
<TR><TD colspan="9"><A HREF="#012">POWER OF ATTORNEY</A></TD></TR>
<TR><TD colspan="9"><A HREF="#013">INDEX TO EXHIBITS</A></TD></TR>
<TR><TD colspan="9"><A HREF="a77350orex5-1.txt">EXHIBIT 5.1</A></TD></TR>
<TR><TD colspan="9"><A HREF="a77350orex23-1.txt">EXHIBIT 23.1</A></TD></TR>
</TABLE>
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<!-- link1 "PART I INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS" -->
<DIV align="left"><A NAME="000"></A></DIV>
<P align="center"><FONT size="2"><B>PART I</B>
</FONT>

<P align="center"><FONT size="2"><B>INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS</B>
</FONT>

<!-- link2 "Item&nbsp;1. Plan Information" -->
<DIV align="left"><A NAME="001"></A></DIV>
<P align="left"><FONT size="2"><B>Item&nbsp;1. Plan Information.</B>*
</FONT>

<!-- link2 "Item&nbsp;2. Registrant Information and Employee Plan Annual Information" -->
<DIV align="left"><A NAME="002"></A></DIV>
<P align="left"><FONT size="2"><B>Item&nbsp;2. Registrant Information and Employee Plan Annual Information.</B>*
</FONT>

<P>
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      <TD width="1%" align="left" nowrap><FONT size="2">*</FONT></TD>
        <TD width="3%"><FONT size="2">&nbsp;</FONT></TD>
        <TD width="96%"><FONT size="2">Information required by Part I to be contained in the Section&nbsp;10(a)
prospectus is omitted from this Registration Statement in accordance with Rule
428 under the Securities act of 1933 and the Note to Part I of Form&nbsp;S-8.</FONT></TD>
</TR>
</TABLE>
<!-- link1 "PART II INFORMATION REQUIRED IN THE REGISTRATION STATEMENT" -->
<DIV align="left"><A NAME="003"></A></DIV>
<P align="center"><FONT size="2"><B>PART II</B>
</FONT>

<P align="center"><FONT size="2"><B>INFORMATION REQUIRED IN THE REGISTRATION STATEMENT</B>
</FONT>

<!-- link2 "Item&nbsp;3. Incorporation of Certain Documents by Reference" -->
<DIV align="left"><A NAME="004"></A></DIV>
<P align="left"><FONT size="2"><B>Item&nbsp;3. Incorporation of Certain Documents by Reference.</B>
</FONT>

<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The following documents filed by Registrant with the Securities and
Exchange Commission (File Nos. 000-31101) are incorporated by reference in
this registration statement:
</FONT>
<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(1)&nbsp; Registrant&#146;s Annual Report on Form&nbsp;10-K for the fiscal year ended
December&nbsp;31, 2000;
</FONT>
<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(2)&nbsp; Registrant&#146;s Quarterly Report on Form&nbsp;10-Q, for the quarters ended
March&nbsp;31, 2001, June&nbsp;30, 2001 and September&nbsp;30,
2001;
</FONT>
<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(3)&nbsp; Registrant&#146;s Periodic Report on Form&nbsp;8-K filed on May&nbsp;11,
2001;
</FONT>
<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(3)&nbsp; The description of Registrant&#146;s Common Stock contained in Registrant&#146;s
registration statement on Form&nbsp;8-A, filed July&nbsp;20, 2000.
</FONT>
<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(4)&nbsp; The description of Registrant&#146;s Preferred Stock Purchase Rights for
Series&nbsp;A Participating Preferred Stock, par value $0.001, contained in
Registrant&#146;s registration statement on Form&nbsp;8-A, filed May&nbsp;11, 2001.
</FONT>
<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;In addition, all documents subsequently filed by Registrant pursuant to
Sections&nbsp;13(a), 13(c), 14 and 15(d) of the Securities Exchange Act of 1934,
prior to the filing of a post-effective amendment which indicates that all
securities offered have been sold or which deregisters all securities then
remaining unsold, shall be deemed to be incorporated by reference in this
registration statement and to be a part hereof from the date of filing of such
documents.
</FONT>
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<DIV align="left"><A NAME="005"></A></DIV>
<P align="left"><FONT size="2"><B>Item&nbsp;4. Description of Securities.</B>
</FONT>

<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not applicable.
</FONT>
<!-- link2 "Item&nbsp;5. Interests of Named Experts and Counsel" -->
<DIV align="left"><A NAME="006"></A></DIV>
<P align="left"><FONT size="2"><B>Item&nbsp;5. Interests of Named Experts and Counsel.</B>
</FONT>

<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Certain legal matters with respect to the validity of the securities
offered hereby has been passed upon by Pillsbury Winthrop LLP. A partner of
Pillsbury Winthrop LLP owns 191,023 shares of Common Stock of the Registrant.
</FONT>
<P align="center"><FONT size="2">-2-</FONT>

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<H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>

<!-- link2 "Item&nbsp;6. Indemnification of Directors and Officers" -->
<DIV align="left"><A NAME="007"></A></DIV>
<P align="left"><FONT size="2"><B>Item&nbsp;6. Indemnification of Directors and Officers.</B>
</FONT>

<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Section&nbsp;145 of the Delaware General Corporation Law provides for the
indemnification of officers, directors, and other corporate agents in terms
sufficiently broad to indemnify such persons under certain circumstances for
liabilities (including reimbursement for expenses incurred) arising under the
Securities Act of 1933, as amended (the &#147;Act&#148;). Article&nbsp;VII of the
Registrant&#146;s Restated Certificate of Incorporation (Exhibit&nbsp;3.(i)2 to the Form
S-1 Registration Agreement) and Article&nbsp;V of the Registrant&#146;s Bylaws (Exhibit
3.(ii)2 to the Form&nbsp;S-1 Registration Agreement) provide for indemnification of
the Registrant&#146;s directors, officers, employees and other agents to the extent
and under the circumstances permitted by the Delaware General Corporation Law.
The Registrant has also entered into agreements with its directors and officers
that will require the Registrant, among other things, to indemnify them against
certain liabilities that may arise by reason of their status or service as
directors or officers to the fullest extent not prohibited by law (Exhibit
10.10 to the Form&nbsp;S-1 Registration Statement).
</FONT>
<!-- link2 "Item&nbsp;7. Exemption from Registration Claimed" -->
<DIV align="left"><A NAME="008"></A></DIV>
<P align="left"><FONT size="2"><B>Item&nbsp;7. Exemption from Registration Claimed.</B>
</FONT>

<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not applicable.
</FONT>
<!-- link2 "Item&nbsp;8. Exhibits" -->
<DIV align="left"><A NAME="009"></A></DIV>
<P align="left"><FONT size="2"><B>Item&nbsp;8. Exhibits.</B>
</FONT>

<P align="left"><FONT size="2">See Index to Exhibits.
</FONT>

<!-- link2 "Item&nbsp;9. Undertakings" -->
<DIV align="left"><A NAME="010"></A></DIV>
<P align="left"><FONT size="2"><B>Item&nbsp;9. Undertakings.</B>
</FONT>

<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(a)&nbsp; The undersigned Registrant hereby undertakes:
</FONT>
<P>
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        <TD width="5%"></TD>
        <TD width="95%"></TD>
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        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(1)&nbsp;To file, during any period in which offers or sales are being
made, a post-effective amendment to this registration statement:</FONT></TD>
</TR>
<TR>
        <TD><FONT size="2">&nbsp;</FONT></TD>
</TR>
<TR valign="top">
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(i)&nbsp;To include any prospectus required by section 10(a)(3) of the
Securities Act of 1933;</FONT></TD>
</TR>
<TR>
        <TD><FONT size="2">&nbsp;</FONT></TD>
</TR>
<TR valign="top">
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(ii)&nbsp;To reflect in the prospectus any facts or events arising after
the effective date of the registration statement (or the most recent
post-effective amendment thereof) which, individually or in the
aggregate, represent a fundamental change in the information set forth in
the registration statement;</FONT></TD>
</TR>
<TR>
        <TD><FONT size="2">&nbsp;</FONT></TD>
</TR>
<TR valign="top">
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(iii)&nbsp;To include any material information with respect to the plan
of distribution not previously disclosed in the registration statement or
any material change to such information in the registration statement;</FONT></TD>
</TR>
</TABLE>
<P>
<TABLE width="100%" border="0" cellpadding="0" cellspacing="0">
<TR valign="top">
        <TD width="1%" align="left" nowrap><FONT size="2">&nbsp;</FONT></TD>
        <TD width="3%"><FONT size="2">&nbsp;</FONT></TD>
        <TD width="96%"><FONT size="2">provided, however, that paragraphs (a)(1)(i) and (a)(1)(ii) do not apply
if the registration statement is on Form&nbsp;S-3 or Form&nbsp;S-8, and the
information required to be included in a post-effective amendment
by those paragraphs is contained in periodic reports filed by the
Registrant pursuant to section 13 or section 15(d) of the
Securities Exchange Act of 1934 that are incorporated by reference
in the registration statement.</FONT></TD>
</TR>
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<P>
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<TR>
        <TD width="5%"></TD>
        <TD width="95%"></TD>
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        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(2)&nbsp;That, for the purpose of determining any liability under the
Securities Act of 1933, each such post-effective amendment shall be
deemed to be a new registration statement relating to the securities
offered therein, and the offering of such securities at that time shall
be deemed to be the initial bona fide offering thereof.</FONT></TD>
</TR>
</TABLE>
<P align="center"><FONT size="2">-3-</FONT>

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<P>
<TABLE width="100%" border="0" cellpadding="0" cellspacing="0">
<TR>
        <TD width="5%"></TD>
        <TD width="95%"></TD>
</TR>
<TR valign="top">
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(3)&nbsp;To remove from registration by means of a post-effective
amendment any of the securities being registered which remain unsold at
the termination of the offering.</FONT></TD>
</TR>
</TABLE>
<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(b)&nbsp; The undersigned Registrant hereby further undertakes that, for
purposes of determining any liability under the Securities Act of 1933, each
filing of the Registrant&#146;s annual report pursuant to section 13(a) or section
15(d) of the Securities Exchange Act of 1934 that is incorporated by reference
in the registration statement shall be deemed to be a new registration
statement relating to the securities offered therein, and the offering of such
securities at that time shall be deemed to be the initial bona fide offering
thereof.
</FONT>
<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(c)&nbsp; Insofar as indemnification for liabilities arising under the
Securities Act of 1933 may be permitted to directors, officers and controlling
persons of the Registrant pursuant to the foregoing provisions, or otherwise,
the Registrant has been advised that in the opinion of the Securities and
Exchange Commission such indemnification is against public policy as expressed
in the Act and is, therefore, unenforceable. In the event that a claim for
indemnification against such liabilities (other than the payment by the
Registrant of expenses incurred or paid by a director, officer or controlling
person of the Registrant in the successful defense of any action, suit or
proceeding) is asserted by such director, officer or controlling person in
connection with the securities being registered, the Registrant will, unless in
the opinion of its counsel the matter has been settled by controlling
precedent, submit to a court of appropriate jurisdiction the question whether
such indemnification by it is against public policy as expressed in the Act and
will be governed by the final adjudication of such issue.
</FONT>
<P align="center"><FONT size="2">-4-</FONT>

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<!-- link1 "SIGNATURES" -->
<DIV align="left"><A NAME="011"></A></DIV>
<P align="center"><FONT size="2"><B>SIGNATURES</B>
</FONT>

<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form&nbsp;S-8, and has duly caused this registration
statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of San Diego, State of California, on November&nbsp;16,
2001.
</FONT>
<CENTER>
<TABLE cellspacing="0" border="0" cellpadding="0" width="100%">
<TR valign="bottom">
        <TD width="59%">&nbsp;</TD>
        <TD width="2%">&nbsp;</TD>
        <TD width="2%">&nbsp;</TD>
        <TD width="2%">&nbsp;</TD>
        <TD width="59%">&nbsp;</TD>
</TR>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD colspan="3" valign="top" align="left"><FONT size="2">APPLIED MOLECULAR EVOLUTION, INC.</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">&nbsp;</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">
By</FONT></TD>

<TD><FONT size="2"></FONT></TD>

<TD align="left" valign="top"><FONT size="2">&#047;s&#047;&nbsp;&nbsp;William D. Huse, M.D., Ph.D.</FONT></TD>
</TR>
<TR>
        <TD valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><HR size="1" noshade></TD>
</TR>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">William D. Huse, M.D., Ph.D.<BR>
President and Chief Executive Officer</FONT></TD>
</TR>
</TABLE>
</CENTER>

<!-- link1 "POWER OF ATTORNEY" -->
<DIV align="left"><A NAME="012"></A></DIV>
<P align="center"><FONT size="2"><B>POWER OF ATTORNEY</B>
</FONT>

<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears
below constitutes and appoints William D. Huse, M.D., Ph.D. and Lawrence E.
Bloch, M.D., J.D., and each of them his true and lawful attorneys-in-fact and
agents, each with full power of substitution and resubstitution, for him and in
his name, place and stead, in any and all capacities, to sign any and all
amendments, including post-effective amendments, to this registration
statement, and to file the same, with exhibits thereto and other documents in
connection therewith, with the Securities and Exchange Commission, granting
unto said attorneys-in-fact and agents, full power and authority to do and
perform each and every act and thing requisite and necessary to be done, as
fully to all intents and purposes as he might or could do in person, hereby
ratifying and confirming all that said attorneys-in-fact and agents, or his
substitute or substitutes, may do or cause to be done by virtue hereof.
</FONT>
<P><FONT size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, this
registration statement has been signed by the following persons in the
capacities and on the date indicated:
</FONT>
<CENTER>
<TABLE cellspacing="0" border="0" cellpadding="0" width="100%">
<TR valign="bottom">
        <TD width="30%">&nbsp;</TD>
        <TD width="5%">&nbsp;</TD>
        <TD width="30%">&nbsp;</TD>
        <TD width="5%">&nbsp;</TD>
        <TD width="30%">&nbsp;</TD>
</TR>
<TR valign="bottom">
        <TD nowrap align="center"><FONT size="1">Name</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center"><FONT size="1">Title</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center"><FONT size="1">Date</FONT></TD>
</TR>
<TR valign="bottom">
        <TD nowrap align="center"><HR size="1" noshade></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center"><HR size="1" noshade></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center"><HR size="1" noshade></TD>
</TR>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&#047;s&#047;&nbsp;&nbsp;William D. Huse, M.D., Ph.D.<BR>
</FONT><HR size="1" noshade><FONT size="2">
William D. Huse, M.D., Ph.D.</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">
Chief Executive Officer,
President and Director
(Principal Executive Officer)
</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>

<TD align="left" valign="top"><FONT size="2">November&nbsp;16, 2001</FONT></TD>
</TR>
<TR><TD><FONT size="2">&nbsp;</FONT></TD></TR>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&#047;s&#047;&nbsp;&nbsp;Lawrence E. Bloch, M.D.<BR>
</FONT><HR size="1" noshade><FONT size="2">
Lawrence E. Bloch, M.D.</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">
Chief Financial Officer,
Vice President, Business
Development and Secretary
(Principal Financial
Officer and Principal
Accounting Officer)
</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">November&nbsp;16, 2001</FONT></TD>
</TR>
</TABLE>
</CENTER>
<P align="center"><FONT size="2">-5-</FONT>

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<CENTER>
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<TR valign="bottom">
        <TD width="30%">&nbsp;</TD>
        <TD width="5%">&nbsp;</TD>
        <TD width="30%">&nbsp;</TD>
        <TD width="5%">&nbsp;</TD>
        <TD width="30%">&nbsp;</TD>
</TR>
<TR valign="bottom">
        <TD nowrap align="center"><FONT size="1">Name</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center"><FONT size="1">Title</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center"><FONT size="1">Date</FONT></TD>
</TR>
<TR valign="bottom">
        <TD nowrap align="center"><HR size="1" noshade></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center"><HR size="1" noshade></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center"><HR size="1" noshade></TD>
</TR>
<TR><TD><FONT size="2">&nbsp;</FONT></TD></TR>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&#047;s&#047;&nbsp;Costa G. Sevastopoulos, Ph.D.<BR>
</FONT><HR size="1" noshade><FONT size="2">
Costa G. Sevastopoulos, Ph.D.</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">
Chairman of the Board
</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">November&nbsp;16, 2001</FONT></TD>
</TR>
<TR><TD><FONT size="2">&nbsp;</FONT></TD></TR>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&#047;s&#047;&nbsp;Stanley T.
Crooke, M.D., Ph.D.<BR>
</FONT><HR size="1" noshade><FONT size="2">
Stanley T. Crooke, M.D., Ph.D.</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">
Director
</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">November&nbsp;16, 2001</FONT></TD>
</TR>
<TR><TD><FONT size="2">&nbsp;</FONT></TD></TR>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&#047;s&#047;&nbsp;Peter K. Hilal, M.D.<BR>
</FONT><HR size="1" noshade><FONT size="2">
Peter K. Hilal, M.D.</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">
Director
</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">November&nbsp;16, 2001</FONT></TD>
</TR>
<TR><TD><FONT size="2">&nbsp;</FONT></TD></TR>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&#047;s&#047;&nbsp;John F. Richards<BR>
</FONT><HR size="1" noshade><FONT size="2">
John F. Richards</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">
Director
</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">November&nbsp;16, 2001</FONT></TD>
</TR>
</TABLE>
</CENTER>
<P align="center"><FONT size="2">-6-</FONT>

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<!-- link1 "INDEX TO EXHIBITS" -->
<DIV align="left"><A NAME="013"></A></DIV>
<P align="center"><FONT size="2"><B>INDEX TO EXHIBITS</B>
</FONT>

<CENTER>
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<TR valign="bottom">
        <TD width="5%">&nbsp;</TD>
        <TD width="2%">&nbsp;</TD>
        <TD width="85%">&nbsp;</TD>
        <TD width="5%">&nbsp;</TD>
        <TD width="1%">&nbsp;</TD>
        <TD width="1%">&nbsp;</TD>
        <TD width="1%">&nbsp;</TD>
</TR>
<TR valign="bottom">
        <TD nowrap align="center"><FONT size="1">Number</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center"><FONT size="1">Exhibit</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
</TR>
<TR valign="bottom">
        <TD nowrap align="center"><HR size="1" noshade></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD nowrap align="center"><HR size="1" noshade></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
        <TD><FONT size="1">&nbsp;</FONT></TD>
</TR>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">4.1*</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">
Specimen Common Stock Certificate.</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">&nbsp;</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">5.1</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">
Opinion regarding legality of securities to be offered.</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">&nbsp;</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">10.1**</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">
Applied Molecular Evolution, Inc. 2001 Stock Incentive Plan.</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">&nbsp;</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">23.1</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">
Consent of Ernst &#038; Young LLP, Independent Auditors.</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">&nbsp;</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">23.2</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">
Consent of Pillsbury Madison &#038; Sutro LLP (included in
Exhibit&nbsp;5.1).</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">&nbsp;</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">&nbsp;</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="bottom">
        <TD valign="top"><FONT size="2">24.1</FONT></TD>
        <TD><FONT size="2">&nbsp;</FONT></TD>
        <TD align="left" valign="top"><FONT size="2">
Power of Attorney (see page 5).</FONT></TD>
</TR>
</TABLE>
</CENTER>
<P>
<HR size="1" width="18%" align="left" noshade>

<TABLE width="100%" border="0" cellpadding="0" cellspacing="0">
<TR valign="top">
      <TD width="1%" align="left" nowrap><FONT size="2">*</FONT></TD>
        <TD width="3%"><FONT size="2">&nbsp;</FONT></TD>
        <TD width="96%"><FONT size="2">Incorporated by reference to
Exhibit&nbsp;4.1 to Registrant&#146;s Registration
Statement on Form&nbsp;S-1, No.&nbsp;333-36830.</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="top">
      <TD width="1%" align="left" nowrap><FONT size="2">&nbsp;</FONT></TD>
        <TD width="3%"><FONT size="2">&nbsp;</FONT></TD>
        <TD width="96%"><FONT size="2">&nbsp;</FONT></TD>
</TR>
<TR><TD><TR><TD><TR><TD><TR><TD>
<TR valign="top">
      <TD width="1%" align="left" nowrap><FONT size="2">**</FONT></TD>
        <TD width="3%"><FONT size="2">&nbsp;</FONT></TD>
        <TD width="96%"><FONT size="2">Incorporated by reference to
Exhibit&nbsp;B to the Registrant&#146;s Proxy Statement
dated April&nbsp;23, 2001.</FONT></TD>
</TR>
</TABLE>




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Applied Molecular Evolution, Inc. Form S-8
Table of Contents
As filed with the Securities and Exchange Commission on November 16, 2001
Registration No. 333-
SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549
Form S-8
REGISTRATION STATEMENT
Under
THE SECURITIES ACT OF 1933
Applied Molecular Evolution, Inc.
(Exact name of registrant as specified in its charter)
Delaware
33-0374014
(State or other jurisdiction of
incorporation or organization)
(I.R.S. Employer Identification No.)
3520 Dunhill Street
San Diego, California
92121
(Address of Principal Executive Offices)
(Zip Code)
2001 STOCK INCENTIVE PLAN
(Full title of the plans)
WILLIAM D. HUSE
President and Chief Executive Officer
Copy to:
3520 Dunhill Street
San Diego, CA 92121
(858) 597-4990
(Name, address and telephone number,
including area code, of agent for service)
THOMAS E. SPARKS, JR.
Pillsbury Winthrop LLP
50 Fremont Street
San Francisco, CA 94120-7880
(415) 983-1000
CALCULATION OF REGISTRATION FEE
Proposed
Maximum
Proposed Maximum
Amount of
Title of Securities to
Amount to be
Offering Price per
Aggregate Offering
Registration
be Registered
Registered(1)
Share(2)
Price(2)
Fee
Common Stock, par value $0.001
500,000 shares
$
8.95
$
4,475,000.00
$
1,118.75
(1)
Pursuant to Rule 416(a) under the Securities Act, this registration
statement also includes an indeterminate number of additional shares which may
be offered and issued in connection with any stock splits, stock dividends or
similar transactions.
(2)
Estimated solely for the purpose of calculating the registration fee
pursuant to Rule 457, based upon the average of the high and low prices as
reported on the Nasdaq National Market on November 12, 2001.
The Registration Statement shall become effective upon filing in
accordance with Rule 462 under the Securities Act of 1933.
TABLE OF CONTENTS
PART I INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS
Item 1. Plan Information
Item 2. Registrant Information and Employee Plan Annual Information
PART II INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
Item 3. Incorporation of Certain Documents by Reference
Item 4. Description of Securities
Item 5. Interests of Named Experts and Counsel
Item 6. Indemnification of Directors and Officers
Item 7. Exemption from Registration Claimed
Item 8. Exhibits
Item 9. Undertakings
SIGNATURES
POWER OF ATTORNEY
INDEX TO EXHIBITS
EXHIBIT 5.1
EXHIBIT 23.1
Table of Contents
PART I
INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS
Item 1. Plan Information.
*
Item 2. Registrant Information and Employee Plan Annual Information.
*
*
Information required by Part I to be contained in the Section 10(a)
prospectus is omitted from this Registration Statement in accordance with Rule
428 under the Securities act of 1933 and the Note to Part I of Form S-8.
PART II
INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
Item 3. Incorporation of Certain Documents by Reference.
The following documents filed by Registrant with the Securities and
Exchange Commission (File Nos. 000-31101) are incorporated by reference in
this registration statement:
(1)  Registrant's Annual Report on Form 10-K for the fiscal year ended
December 31, 2000;
(2)  Registrant's Quarterly Report on Form 10-Q, for the quarters ended
March 31, 2001, June 30, 2001 and September 30,
2001;
(3)  Registrant's Periodic Report on Form 8-K filed on May 11,
2001;
(3)  The description of Registrant's Common Stock contained in Registrant's
registration statement on Form 8-A, filed July 20, 2000.
(4)  The description of Registrant's Preferred Stock Purchase Rights for
Series A Participating Preferred Stock, par value $0.001, contained in
Registrant's registration statement on Form 8-A, filed May 11, 2001.
In addition, all documents subsequently filed by Registrant pursuant to
Sections 13(a), 13(c), 14 and 15(d) of the Securities Exchange Act of 1934,
prior to the filing of a post-effective amendment which indicates that all
securities offered have been sold or which deregisters all securities then
remaining unsold, shall be deemed to be incorporated by reference in this
registration statement and to be a part hereof from the date of filing of such
documents.
Item 4. Description of Securities.
Not applicable.
Item 5. Interests of Named Experts and Counsel.
Certain legal matters with respect to the validity of the securities
offered hereby has been passed upon by Pillsbury Winthrop LLP. A partner of
Pillsbury Winthrop LLP owns 191,023 shares of Common Stock of the Registrant.
-2-
Table of Contents
Item 6. Indemnification of Directors and Officers.
Section 145 of the Delaware General Corporation Law provides for the
indemnification of officers, directors, and other corporate agents in terms
sufficiently broad to indemnify such persons under certain circumstances for
liabilities (including reimbursement for expenses incurred) arising under the
Securities Act of 1933, as amended (the "Act"). Article VII of the
Registrant's Restated Certificate of Incorporation (Exhibit 3.(i)2 to the Form
S-1 Registration Agreement) and Article V of the Registrant's Bylaws (Exhibit
3.(ii)2 to the Form S-1 Registration Agreement) provide for indemnification of
the Registrant's directors, officers, employees and other agents to the extent
and under the circumstances permitted by the Delaware General Corporation Law.
The Registrant has also entered into agreements with its directors and officers
that will require the Registrant, among other things, to indemnify them against
certain liabilities that may arise by reason of their status or service as
directors or officers to the fullest extent not prohibited by law (Exhibit
10.10 to the Form S-1 Registration Statement).
Item 7. Exemption from Registration Claimed.
Not applicable.
Item 8. Exhibits.
See Index to Exhibits.
Item 9. Undertakings.
(a)  The undersigned Registrant hereby undertakes:
(1) To file, during any period in which offers or sales are being
made, a post-effective amendment to this registration statement:
(i) To include any prospectus required by section 10(a)(3) of the
Securities Act of 1933;
(ii) To reflect in the prospectus any facts or events arising after
the effective date of the registration statement (or the most recent
post-effective amendment thereof) which, individually or in the
aggregate, represent a fundamental change in the information set forth in
the registration statement;
(iii) To include any material information with respect to the plan
of distribution not previously disclosed in the registration statement or
any material change to such information in the registration statement;
provided, however, that paragraphs (a)(1)(i) and (a)(1)(ii) do not apply
if the registration statement is on Form S-3 or Form S-8, and the
information required to be included in a post-effective amendment
by those paragraphs is contained in periodic reports filed by the
Registrant pursuant to section 13 or section 15(d) of the
Securities Exchange Act of 1934 that are incorporated by reference
in the registration statement.
(2) That, for the purpose of determining any liability under the
Securities Act of 1933, each such post-effective amendment shall be
deemed to be a new registration statement relating to the securities
offered therein, and the offering of such securities at that time shall
be deemed to be the initial bona fide offering thereof.
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(3) To remove from registration by means of a post-effective
amendment any of the securities being registered which remain unsold at
the termination of the offering.
(b)  The undersigned Registrant hereby further undertakes that, for
purposes of determining any liability under the Securities Act of 1933, each
filing of the Registrant's annual report pursuant to section 13(a) or section
15(d) of the Securities Exchange Act of 1934 that is incorporated by reference
in the registration statement shall be deemed to be a new registration
statement relating to the securities offered therein, and the offering of such
securities at that time shall be deemed to be the initial bona fide offering
thereof.
(c)  Insofar as indemnification for liabilities arising under the
Securities Act of 1933 may be permitted to directors, officers and controlling
persons of the Registrant pursuant to the foregoing provisions, or otherwise,
the Registrant has been advised that in the opinion of the Securities and
Exchange Commission such indemnification is against public policy as expressed
in the Act and is, therefore, unenforceable. In the event that a claim for
indemnification against such liabilities (other than the payment by the
Registrant of expenses incurred or paid by a director, officer or controlling
person of the Registrant in the successful defense of any action, suit or
proceeding) is asserted by such director, officer or controlling person in
connection with the securities being registered, the Registrant will, unless in
the opinion of its counsel the matter has been settled by controlling
precedent, submit to a court of appropriate jurisdiction the question whether
such indemnification by it is against public policy as expressed in the Act and
will be governed by the final adjudication of such issue.
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SIGNATURES
Pursuant to the requirements of the Securities Act of 1933, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-8, and has duly caused this registration
statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of San Diego, State of California, on November 16,
2001.
APPLIED MOLECULAR EVOLUTION, INC.
By
/s/  William D. Huse, M.D., Ph.D.
William D. Huse, M.D., Ph.D.
President and Chief Executive Officer
POWER OF ATTORNEY
KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears
below constitutes and appoints William D. Huse, M.D., Ph.D. and Lawrence E.
Bloch, M.D., J.D., and each of them his true and lawful attorneys-in-fact and
agents, each with full power of substitution and resubstitution, for him and in
his name, place and stead, in any and all capacities, to sign any and all
amendments, including post-effective amendments, to this registration
statement, and to file the same, with exhibits thereto and other documents in
connection therewith, with the Securities and Exchange Commission, granting
unto said attorneys-in-fact and agents, full power and authority to do and
perform each and every act and thing requisite and necessary to be done, as
fully to all intents and purposes as he might or could do in person, hereby
ratifying and confirming all that said attorneys-in-fact and agents, or his
substitute or substitutes, may do or cause to be done by virtue hereof.
Pursuant to the requirements of the Securities Act of 1933, this
registration statement has been signed by the following persons in the
capacities and on the date indicated:
Name
Title
Date
/s/  William D. Huse, M.D., Ph.D.
William D. Huse, M.D., Ph.D.
Chief Executive Officer,
President and Director
(Principal Executive Officer)
November 16, 2001
/s/  Lawrence E. Bloch, M.D.
Lawrence E. Bloch, M.D.
Chief Financial Officer,
Vice President, Business
Development and Secretary
(Principal Financial
Officer and Principal
Accounting Officer)
November 16, 2001
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Name
Title
Date
/s/ Costa G. Sevastopoulos, Ph.D.
Costa G. Sevastopoulos, Ph.D.
Chairman of the Board
November 16, 2001
/s/ Stanley T.
Crooke, M.D., Ph.D.
Stanley T. Crooke, M.D., Ph.D.
Director
November 16, 2001
/s/ Peter K. Hilal, M.D.
Peter K. Hilal, M.D.
Director
November 16, 2001
/s/ John F. Richards
John F. Richards
Director
November 16, 2001
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INDEX TO EXHIBITS
Number
Exhibit
4.1*
Specimen Common Stock Certificate.
5.1
Opinion regarding legality of securities to be offered.
10.1**
Applied Molecular Evolution, Inc. 2001 Stock Incentive Plan.
23.1
Consent of Ernst & Young LLP, Independent Auditors.
23.2
Consent of Pillsbury Madison & Sutro LLP (included in
Exhibit 5.1).
24.1
Power of Attorney (see page 5).
*
Incorporated by reference to
Exhibit 4.1 to Registrant's Registration
Statement on Form S-1, No. 333-36830.
**
Incorporated by reference to
Exhibit B to the Registrant's Proxy Statement
dated April 23, 2001.