Table 1.

The data set used to assess SiteLight’s ability to predict sites

No.	Target mol.	Template protein	Complex	Targ. chain	Temp. chain	ASPD entry	Library size	Seq. leng.	Library type
Protein–Protein
1A	Bovine Hsc70	Bag chaperone regulator1	1HX1	A	B	PH1PO059	8	15	I
1B	Bovine Hsc70	Bag chaperone regulator1	1HX1	A	B	H1PO059	3	6	I
2	subtilisin	eglinC	1CSE	E	I	PH1BS037	18	5	I
3	Factor VIIa	soluble tissue factor	1DAN	LH	TU	PH1BS102	34	11	V
4	Fyn SH3	V1 Nef	1AVZ	C	AB	PH1BS005	18	11	I
5	Nef	Hck-SH3	1AVZ	AB	C	PH1PO057	19	6	II
6A	Kallikrein	Hirustasin	1HIA	AB	I	PH1PO062	18	6	IV
6B	Kallikrein	Hirustasin	1HIA	AB	I	PH1PO063	11	6	IV
7	plasmin	streptokinase	1BML	A	C	PH1NE002	32	7	V
8	Human α thrombin	Haemadin	1E0F	AD	I	PH1PO064	11	6	IV
9A	Bovine trypsin	APPI	1TAW	A	B	PH1VV009	6	3	II
9B	Bovine trypsin	APPI	1TAW	A	B	PH1VV010	11	3	II
9C	Bovine trypsin	APPI	1TAW	A	B	PH1VV011	12	3	II
10	Actine	Deoxyribonuclease I	1ATN	A	D	Jesaitis	29	9	Ia
11	Rat trypsin	Ecotin	1F5R	A	I	PH1BS201	14	4	II
Dimers
12	ubiquitin	ubiquitin	1AAR	B	A	PH1NE004	6	5	IV
13A	glutathione transferase	glutathione transferase	1GSD	B	A	PH1NE003	20	5	II
13B	glutathione transferase	glutathione transferase	1GSD	B	A	PH1NE003	6	15	II
14	SH3	SH2	1G83	A	B	PH1BS005	18	11	I
Peptide–Protein
15	Peptide	Plasminogen activator	1C5X	A	B	PH1VV018	91	6	I
Antigen–Antibody
16A	GP120	Ab 17B	1G9M	G	LH	PH1BS014	13	13	Ib
16B	GP120	Ab 17B	1G9M	G	LH	Ferrer	10	7	I
17A	VEGF	VEGF Ab (CDR H1)	1BJ1	V	LH	PH1PO091	6	6	I
17B	VEGF	VEGF Ab (CDR H2)	1BJ1	V	LH	PH1PO092	5	5	I
17C	VEGF	VEGF Ab (CDR H3)	1BJ1	V	LH	PH1PO093	31	6	I
18A	A6	Interferon gamma receptor	1JRH	LH	I	Lang	23	5	III
18B	A6	Interferon gamma receptor	1JRH	LH	I	Lang	7	5	III
18C	A6	Interferon gamma receptor	1JRH	LH	I	Lang	36	5	III
Antigen–Fc
19A	h IGg FC	Fragment B of protein A	1FC2	D	C	DeLano	2	20	I
19B	h IGg FC	Protein G C2	1FCC	A	C	DeLano	2	20	I
19C	h IGg FC	h IGM Rheumatoid factor	1ADQ	A	LH	DeLano	2	20	I
19D	h IGg FC	Fc receptor (Neunatanl)	1FRT	A	B	DeLano	2	20	I
20	IgM rheumatoid factor	Human IGg FC	1ADQ	LH	A	DeLano	12	10	I
Hapten–Antobody
21	Fluorescein	4-4-20 FAb	4FAB	Hetero	LH	PH1PO122	4	4	II
22A	Digoxin	26-10 FAb	1IGJ	X	AB	PH1VV021	20	6	II
22B	Digoxin	26-10 FAb	1IGJ	X	AB	PH1VV022	2	6	II
22C	Digoxin	26-10 FAb	1IGJ	X	AB	PH1VV023	7	6	II
22D	Digoxin	26-10 FAb	1IGJ	X	AB	PH1VV024	8	6	II
Inhibitor/s–Enzyme
23A	S-Benzyl-Glutathione	Glutathione transferase A1	1GUH	Hetero	A	PH1NE003	11	5	II
23B	S-Benzyl-Glutathione	Glutathione transferase A1	1GUH	Hetero	A	PH1NE003	8	15	II
Receptor–Hormone
24A	h Growth hormone	Growth hormone receptor	3HHR	BC	A	PH1BS006	24	20	II
24B	h Growth hormone	Growth hormone receptor	3HHR	BC	A	PH1BS007	16	20	II
24C	h Growth hormone	Growth hormone receptor	3HHR	BC	A	PH1BS008	7	20	II

The definitions of Target, Template, and Library Types are given in the text and in Figure 1▶. Library size indicates the number of phage display library derived peptides. Sequence length (Seq. leng.) indicates the average number of amino acids in a peptide in the library. Library peptides have similar lengths. Redundant cases (i.e, complexes with more than one library and libraries with more than one complex) are denoted by the same serial number. They are distinguished by capital letters. The complex code refers to the Protein Data Bank (Berman et al. 2000). The ASPD entry is from Valuev et al. (2002). Where not present in the ASPD database, these were searched and taken from the literature. (Ferrer = Ferrer and Harrison 1999; Jesaitis = Jesaitis et al. 1999; Lang = Lang et al. 2000; DeLano = DeLano et al. 2000).

^a Library formed in diluted antiserm.

^b An antibody library prepared from bone marrow lymphocytes.