AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON DECEMBER 7, 2000

REGISTRATION NO. 333-32298
- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------

SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549
------------------------

AMENDMENT NO. 2

FORM S-1
REGISTRATION STATEMENT
UNDER
THE SECURITIES ACT OF 1933

NETGENICS, INC.
(EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

DELAWARE 7371 34-1834775
(STATE OR OTHER JURISDICTION OF (PRIMARY STANDARD INDUSTRIAL (I.R.S. EMPLOYER
INCORPORATION OR ORGANIZATION) CLASSIFICATION CODE NUMBER) IDENTIFICATION NUMBER)

1717 EAST NINTH STREET, SUITE 1600
CLEVELAND, OHIO 44114
TELEPHONE: (216) 861-4007
(ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE, OF
REGISTRANT'S PRINCIPAL EXECUTIVE OFFICES)

VINCENT P. KAZMER
EXECUTIVE VICE PRESIDENT AND CHIEF FINANCIAL OFFICER
1717 EAST NINTH STREET, SUITE 1600
CLEVELAND, OHIO 44114
TELEPHONE: (216) 861-4007
(NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE,
OF AGENT FOR SERVICE)

COPIES TO:

CHRISTOPHER M. KELLY, ESQ. ERIN E. KARZMER, ESQ. WILLIAM T. WHELAN, ESQ.
JONES, DAY, REAVIS & POGUE JONES, DAY, REAVIS & POGUE JOSEPH E. MULLANEY III, ESQ.
599 LEXINGTON AVENUE, 32ND FLOOR NORTH POINT MINTZ, LEVIN, COHN, FERRIS,
NEW YORK, NEW YORK 10022 901 LAKESIDE AVENUE GLOVSKY AND POPEO, P.C.
TEL: (212) 326-3939 CLEVELAND, OHIO 44114 ONE FINANCIAL CENTER
FAX: (212) 755-7306 TEL: (216) 586-3939 BOSTON, MASSACHUSETTS 02111
FAX: (216) 579-0212 TEL: (617) 542-6000
FAX: (617) 542-2241

APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:

As soon as practicable after this Registration Statement becomes effective.

If any of the securities being registered on this Form are to be offered on
a delayed or continuous basis pursuant to Rule 415 under the Securities Act,
check the following box. [ ]

If this Form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act, check the following box and
list the Securities Act registration statement number of the earlier effective
registration statement for the same offering. [ ] __________

If this Form is a post-effective amendment filed pursuant to Rule 462(c)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. [ ] __________

If this Form is a post-effective amendment filed pursuant to Rule 462(d)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. [ ] __________

If delivery of the prospectus is expected to be made pursuant to Rule 434,
check the following box. [ ]

THE REGISTRANT HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR
DATES AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT SHALL
FILE A FURTHER AMENDMENT WHICH SPECIFICALLY STATES THAT THIS REGISTRATION
STATEMENT SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(a) OF
THE SECURITIES ACT OF 1933 OR UNTIL THIS REGISTRATION STATEMENT SHALL BECOME
EFFECTIVE ON SUCH DATE AS THE COMMISSION, ACTING PURSUANT TO SAID SECTION 8(a),
MAY DETERMINE.

- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------
2

EXPLANATORY NOTE

This amendment no. 2 is filed solely for the purpose of adding certain
exhibits not previously filed and refiling an exhibit previously filed to
include the appendices to such exhibit.

ITEM 16. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES.

EXHIBIT
NUMBER DESCRIPTION OF DOCUMENT
- ----- ------------------------------------------------------------

*1.1 Form of Underwriting Agreement
+3.1 Certificate of Incorporation
+3.2 Bylaws
3.3 Form of Amended and Restated Certificate of Incorporation
3.4 Form of Amended and Restated Bylaws
+4.1 NetGenics, Inc. Stock Purchase Warrant, dated as of October
18, 1999, by and between NetGenics, Inc. and International
Business Machines Corporation
4.2 Amended and Restated Registration Rights Agreement, dated as
of December 21, 1999, by and among NetGenics, Inc. and the
stockholders named therein
*5.1 Opinion of Jones, Day, Reavis & Pogue
+10.1 Form of D&O Indemnification Agreement between NetGenics,
Inc. and its directors and certain executive officers
+10.2 Registrant's 1996 Stock Option Plan
+10.3 Employment Agreement, dated as of June 25, 1996, by and
between Manuel J. Glynias and NetGenics, Inc.
+10.4 Employment Agreement, dated as of November 10, 1999, by and
between NetGenics, Inc. and Vincent P. Kazmer
+10.5 Technical Services Agreement, dated as of October 15, 1999,
by and between International Business Machines Corporation
and NetGenics, Inc.
10.6 Intentionally omitted
++10.7 SYNERGY Software License and Subscription Agreement, dated
as of April 2, 1999, by and between NetGenics International,
Ltd. and Aventis CropScience (formerly Hoescht Schering
AgrEvo GmbH)
+21.1 Subsidiaries of NetGenics, Inc.
+23.1 Consent of PricewaterhouseCoopers LLP
*23.2 Consent of Jones, Day, Reavis & Pogue (included in Exhibit
5.1)
+24.1 Powers of Attorney
+27.1 Financial Data Schedule
+27.2 Financial Data Schedule
+27.3 Financial Data Schedule
+27.4 Financial Data Schedule

- ---------------

* To be filed by amendment

++ Confidential treatment requested as to certain portions, which portions have
been omitted and filed separately with the SEC.

+ Previously filed.

II-4
4

SIGNATURES

Pursuant to the requirements of the Securities Act of 1933, NetGenics, Inc.
has duly caused this amendment no. 2 to the registration statement to be signed
on its behalf by the undersigned, thereunto duly authorized, in the city of
Cleveland, State of Ohio, on December 7, 2000.

NETGENICS, INC.

By: /s/ VINCENT P. KAZMER

------------------------------------

Vincent P. Kazmer

Executive Vice President and
Chief Financial Officer

Pursuant to the requirements of the Securities Act of 1933, this amendment
no. 2 to the registration statement has been signed on December 7, 2000 by the
following persons in the capacities indicated.

SIGNATURE TITLE
--------- -----

* Chief Executive Officer and Director
- ----------------------------------------------------- (Principal Executive Officer)
Manuel J. Glynias

/s/ VINCENT P. KAZMER Chief Financial Officer
- ----------------------------------------------------- (Principal Financial Officer and Principal
Vincent P. Kazmer Accounting Officer)

* Director
- -----------------------------------------------------
Walter Gilbert

* Director
- -----------------------------------------------------
Anthony B. Evnin

* Director
- -----------------------------------------------------
John Pappajohn

* Director
- -----------------------------------------------------
Nicole Vitullo

* Director
- -----------------------------------------------------
Alan G. Walton

* Vincent P. Kazmer, by signing his name hereto, does hereby execute this
amendment no. 2 to the registration statement on behalf of the directors and
officers of the Registrant indicated above by asterisks, pursuant to powers of
attorney duly executed by such directors and officers, which are filed
herewith with the Securities and Exchange Commission on behalf of such
directors and officers.