-----BEGIN PRIVACY-ENHANCED MESSAGE----- Proc-Type: 2001,MIC-CLEAR Originator-Name: webmaster@www.sec.gov Originator-Key-Asymmetric: MFgwCgYEVQgBAQICAf8DSgAwRwJAW2sNKK9AVtBzYZmr6aGjlWyK3XmZv3dTINen TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB MIC-Info: RSA-MD5,RSA, CLhR11K1mMk+BLs1ci3YEzCvk1DILEP+zjdD+B8XW+9AmueeozYR8Ur/pvLyq0qP 1UaBA9NL99NC+HXqf+ZlPQ== 0000912057-02-034780.txt : 20020906 0000912057-02-034780.hdr.sgml : 20020906 20020906163849 ACCESSION NUMBER: 0000912057-02-034780 CONFORMED SUBMISSION TYPE: SC 13G/A PUBLIC DOCUMENT COUNT: 2 FILED AS OF DATE: 20020906 GROUP MEMBERS: BIOTECHNOLOGY VALUE FUND II, L.P. GROUP MEMBERS: BVF INC. GROUP MEMBERS: BVF INVESTMENTS, L.L.C. GROUP MEMBERS: BVF PARTNERS L.P. SUBJECT COMPANY: COMPANY DATA: COMPANY CONFORMED NAME: APPLIED MOLECULAR EVOLUTION INC CENTRAL INDEX KEY: 0001111312 STANDARD INDUSTRIAL CLASSIFICATION: SERVICES-COMMERCIAL PHYSICAL & BIOLOGICAL RESEARCH [8731] IRS NUMBER: 330374014 STATE OF INCORPORATION: DE FISCAL YEAR END: 1231 FILING VALUES: FORM TYPE: SC 13G/A SEC ACT: 1934 Act SEC FILE NUMBER: 005-59733 FILM NUMBER: 02758740 BUSINESS ADDRESS: STREET 1: 3520 DUNHILL STREET CITY: SAN DIEGO STATE: CA ZIP: 92121 BUSINESS PHONE: 5855974990 MAIL ADDRESS: STREET 1: 3520 DUNHILL STREET CITY: SAN DIEGO STATE: CA ZIP: 92121 FILED BY: COMPANY DATA: COMPANY CONFORMED NAME: BIOTECHNOLOGY VALUE FUND L P CENTRAL INDEX KEY: 0000918923 STANDARD INDUSTRIAL CLASSIFICATION: INVESTMENT ADVICE [6282] IRS NUMBER: 363924731 STATE OF INCORPORATION: DE FILING VALUES: FORM TYPE: SC 13G/A BUSINESS ADDRESS: STREET 1: 227 W MONROE STREET, SUITE 4800 STREET 2: 227 W MONROE STREET, SUITE 4800 CITY: CHICAGO STATE: IL ZIP: 60606 BUSINESS PHONE: 415-288-23 MAIL ADDRESS: STREET 1: 227 W MONROE STREET, SUITE 4800 STREET 2: 227 W MONROE STREET, SUITE 4800 CITY: CHICAGO STATE: IL ZIP: 60606 SC 13G/A 1 a2088816zsc13ga.htm SC 13G/A
QuickLinks -- Click here to rapidly navigate through this document

SECURITIES AND EXCHANGE COMMISSION
Washington, DC 20549

SCHEDULE 13G
(Rule 13d-102)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT
TO RULES 13d-1(b) (c) AND (d) AND AMENDMENTS THERETO FILED
PURSUANT TO 13d-2(b)
(Amendment No. 2)¹

Applied Molecular Evolution, Inc.
(Name of Issuer)

Common Stock
(Title of Class of Securities)

03823E 10 8
(CUSIP Number)

September 3, 2002
(Date of Event Which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule is filed:

o        Rule 13d-1(b)
ý        Rule 13d-1(c)
o        Rule 13d-1(d)

¹ The remainder of this cover page shall be filled out for a reporting person's initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange Act of 1934 or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

CUSIP NO. 03823E 10 8

13G

Page 2 of 9 Pages


1	NAME OF REPORTING PERSON: Biotechnology Value Fund, L.P.
	I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
		(a) ý
		(b) o

3	SEC USE ONLY


4	CITIZENSHIP OR PLACE OF ORGANIZATION
	Delaware

	5	SOLE VOTING POWER
NUMBER OF		0
SHARES
BENEFICIALLY	6	SHARED VOTING POWER
OWNED		725,200
BY
EACH	7	SOLE DISPOSITIVE POWER
REPORTING		0
PERSON
WITH	8	SHARED DISPOSITIVE POWER
		725,200


9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
	725,200

10	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*
		o

11	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
	3.1%

12	TYPE OF REPORTING PERSON*
	PN

* SEE INSTRUCTIONS BEFORE FILLING OUT!

CUSIP NO. 03823E 10 8

13G

Page 3 of 9 Pages


1	NAME OF REPORTING PERSON: Biotechnology Value Fund II, L.P.
	I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
		(a) ý
		(b) o

3	SEC USE ONLY


4	CITIZENSHIP OR PLACE OF ORGANIZATION
	Delaware

	5	SOLE VOTING POWER
NUMBER OF		0
SHARES
BENEFICIALLY	6	SHARED VOTING POWER
OWNED		473,700
BY
EACH	7	SOLE DISPOSITIVE POWER
REPORTING		0
PERSON
WITH	8	SHARED DISPOSITIVE POWER
		473,700


9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
	473,700

10	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*
		o

11	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
	2.0%

12	TYPE OF REPORTING PERSON*
	PN

* SEE INSTRUCTIONS BEFORE FILLING OUT!

CUSIP NO. 03823E 10 8

13G

Page 4 of 9 Pages


1	NAME OF REPORTING PERSON: BVF Investments, L.L.C.
	I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
		(a) ý
		(b) o

3	SEC USE ONLY


4	CITIZENSHIP OR PLACE OF ORGANIZATION
	Delaware

	5	SOLE VOTING POWER
NUMBER OF		0
SHARES
BENEFICIALLY	6	SHARED VOTING POWER
OWNED		1,089,192
BY
EACH	7	SOLE DISPOSITIVE POWER
REPORTING		0
PERSON
WITH	8	SHARED DISPOSITIVE POWER
		1,089,192


9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
	1,089,192

10	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*
		o

11	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
	4.6%

12	TYPE OF REPORTING PERSON*
	OO

* SEE INSTRUCTIONS BEFORE FILLING OUT!

CUSIP NO. 03823E 10 8

13G

Page 5 of 9 Pages


1	NAME OF REPORTING PERSON: BVF Partners L.P.
	I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
		(a) ý
		(b) o

3	SEC USE ONLY


4	CITIZENSHIP OR PLACE OF ORGANIZATION
	Delaware

	5	SOLE VOTING POWER
NUMBER OF		0
SHARES
BENEFICIALLY	6	SHARED VOTING POWER
OWNED		2,375,592
BY
EACH	7	SOLE DISPOSITIVE POWER
REPORTING		0
PERSON
WITH	8	SHARED DISPOSITIVE POWER
		2,375,592


9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
	2,375,592

10	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*
		o

11	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
	10.1%

12	TYPE OF REPORTING PERSON*
	PN

* SEE INSTRUCTIONS BEFORE FILLING OUT!

CUSIP NO. 03823E 10 8

13G

Page 6 of 9 Pages


1	NAME OF REPORTING PERSON: BVF Inc.
	I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
		(a) ý
		(b) o

3	SEC USE ONLY


4	CITIZENSHIP OR PLACE OF ORGANIZATION
	Delaware

	5	SOLE VOTING POWER
NUMBER OF		0
SHARES
BENEFICIALLY	6	SHARED VOTING POWER
OWNED		2,375,592
BY
EACH	7	SOLE DISPOSITIVE POWER
REPORTING		0
PERSON
WITH	8	SHARED DISPOSITIVE POWER
		2,375,592


9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
	2,375,592

10	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*
		o

11	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
	10.1%

12	TYPE OF REPORTING PERSON*
	IA, CO

* SEE INSTRUCTIONS BEFORE FILLING OUT!

CUSIP NO. 03823E 10 8

13G

Page 7 of 9 Pages

ITEM 1(a). NAME OF ISSUER:

Applied Molecular Evolution, Inc. ("Applied Molecular Evolution")

ITEM 1(b). ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES:

3520 Dunhill Street
San Diego, California 92121

ITEM 2(a). NAME OF PERSON FILING:

This Amendment to Schedule 13G is being filed on behalf of the following persons* (the "Reporting Persons"):

(i): Biotechnology Value Fund, L.P. ("BVF")
(ii): Biotechnology Value Fund II, L.P. ("BVF2")
(iii): BVF Investments, L.L.C. ("Investments")
(iv): BVF Partners L.P. ("Partners")
(v): BVF Inc. ("BVF Inc.")
*: Attached as Exhibit 1 is a copy of an agreement among the Reporting Persons filing (as specified hereinabove) that this Amendment to Schedule 13G is being filed on behalf of each of them.

ITEM 2(b). ADDRESS OF PRINCIPAL BUSINESS OFFICE:

The principal business office of the Reporting Persons comprising the group filing this Amendment to Schedule 13G is located at 227 West Monroe Street, Suite 4800, Chicago, Illinois, 60606.

ITEM 2(c). CITIZENSHIP:

BVF:		a Delaware limited partnership
BVF2:		a Delaware limited partnership
Investments:		a Delaware limited liability company
Partners:		a Delaware limited partnership
BVF Inc.:		a Delaware corporation

ITEM 2(d). TITLE OF CLASS OF SECURITIES:

Common Stock.

ITEM 2(e). CUSIP Number:

03823E 10 8

CUSIP NO. 03823E 10 8

13G

Page 8 of 9 Pages

ITEM 3. IF THIS STATEMENT IS FILED PURSUANT TO RULE 13d-1(b), or 13d-2(b) or (c) CHECK WHETHER
THE PERSON FILING IS: One of the following

Not applicable as this Amendment to Schedule 13G is filed pursuant to Rule 13d 1(c).

ITEM 4. OWNERSHIP:

The information in items 1 and 5 through 11 on the cover pages (pp. 2 - 6) on this Amendment to Schedule 13G is hereby incorporated by reference.

ITEM 5. OWNERSHIP OF FIVE PERCENT OR LESS OF A CLASS:

If this statement is being filed to report the fact that as of the date hereof the Reporting Persons have ceased to be the beneficial owner of more than five percent of the class of securities check the following. o

ITEM 6. OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER PERSON:

BVF shares voting and dispositive power over the shares of the common stock it beneficially owns with Partners. BVF2 also shares voting and dispositive power over the shares of the common stock it beneficially owns with Partners. Investments also shares voting and dispositive power over the shares of the common stock it beneficially owns with Partners. Partners and BVF Inc. share voting and dispositive power over the shares of the common stock they beneficially own with, in addition to BVF, BVF2 and Investments, certain managed accounts on whose behalf Partners, as investment manager, purchased such shares. None of the managed accounts individually owns more than 5% of the common stock of Applied Molecular Evolution.

ITEM 7. IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH ACQUIRED THE
SECURITY BEING REPORTED ON BY THE PARENT HOLDING COMPANY:

Not applicable.

ITEM 8. IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF A GROUP:

Not applicable.

ITEM 9. NOTICE OF DISSOLUTION OF GROUP:

Not applicable.

CUSIP NO. 03823E 10 8

13G

Page 9 of 9 Pages

ITEM 10. CERTIFICATION

By signing below I certify that, to the best of my knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect.

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Dated: September 6, 2002

BIOTECHNOLOGY VALUE FUND, L.P.
By:	BVF Partners L.P., its general partner
	By:	BVF Inc., its general partner
		By:	/s/ MARK N. LAMPERT Mark N. Lampert President
BIOTECHNOLOGY VALUE FUND II, L.P.
By:	BVF Partners L.P., its general partner
	By:	BVF Inc., its general partner
		By:	/s/ MARK N. LAMPERT Mark N. Lampert President
BVF INVESTMENTS, L.L.C.
By:	BVF Partners L.P., its manager
	By:	BVF Inc., its general partner
		By:	/s/ MARK N. LAMPERT Mark N. Lampert President
BVF PARTNERS L.P.
By:	BVF Inc., its general partner
	By:	/s/ MARK N. LAMPERT Mark N. Lampert President
BVF INC.
By:	/s/ MARK N. LAMPERT Mark N. Lampert President

QuickLinks

SCHEDULE 13G
ITEM 1(a). NAME OF ISSUER
ITEM 1(b). ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES
ITEM 2(a). NAME OF PERSON FILING
ITEM 2(b). ADDRESS OF PRINCIPAL BUSINESS OFFICE
ITEM 2(c). CITIZENSHIP
ITEM 2(d). TITLE OF CLASS OF SECURITIES
ITEM 2(e). CUSIP Number
ITEM 3. IF THIS STATEMENT IS FILED PURSUANT TO RULE 13d-1(b), or 13d-2(b) or (c) CHECK WHETHER THE PERSON FILING IS: One of the following
ITEM 4. OWNERSHIP
ITEM 5. OWNERSHIP OF FIVE PERCENT OR LESS OF A CLASS
ITEM 6. OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER PERSON
ITEM 7. IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH ACQUIRED THE SECURITY BEING REPORTED ON BY THE PARENT HOLDING COMPANY
ITEM 8. IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF A GROUP
ITEM 9. NOTICE OF DISSOLUTION OF GROUP
ITEM 10. CERTIFICATION
EX-1 3 a2088816zex-1.htm EXHIBIT 1
QuickLinks -- Click here to rapidly navigate through this document

EXHIBIT 1

AGREEMENT REGARDING JOINT FILING

The undersigned, Biotechnology Value Fund, L.P., a Delaware limited partnership, Biotechnology Value Fund II, L.P., a Delaware limited partnership, BVF Investments, L.L.C., a Delaware limited liability company, BVF Partners L.P., a Delaware limited partnership, and BVF Inc., a Delaware corporation, hereby agree and acknowledge that the information required by Amendment to Schedule 13G, to which this Agreement is attached as an exhibit, is filed on behalf of each of them. The undersigned further agree that any amendments or supplements thereto shall also be filed on behalf of each of them.

Dated: September 6, 2002

BIOTECHNOLOGY VALUE FUND, L.P.
By:	BVF Partners L.P., its general partner
	By:	BVF Inc., its general partner
		By:	/s/ MARK N. LAMPERT Mark N. Lampert President
BIOTECHNOLOGY VALUE FUND II, L.P.
By:	BVF Partners L.P., its general partner
	By:	BVF Inc., its general partner
		By:	/s/ MARK N. LAMPERT Mark N. Lampert President
BVF INVESTMENTS, L.L.C.
By:	BVF Partners L.P., its manager
	By:	BVF Inc., its general partner
		By:	/s/ MARK N. LAMPERT Mark N. Lampert President
BVF PARTNERS L.P.
By:	BVF Inc., its general partner
	By:	/s/ MARK N. LAMPERT Mark N. Lampert President
BVF INC.
By:	/s/ MARK N. LAMPERT Mark N. Lampert President

QuickLinks

EXHIBIT 1
AGREEMENT REGARDING JOINT FILING
-----END PRIVACY-ENHANCED MESSAGE-----