Table 4.

Searching the database of binding sites with a complete protein structure of a fatty acid-binding protein (1lib)

Rank	PDB	Protein	Fold	Sequence similarity (%)	Match score	Ligand	RMSD	Run time (seconds)
1	1lib	Adipocyte lipid-binding protein (ALBP)	Lipocalins	100	100	None∗	N/A	7
2	1lid	Adipocyte lipid-binding protein (ALBP)	Lipocalins	100	72	OLA∗	0.2	14.2
3	1lie	Adipocyte lipid-binding protein (ALBP)	Lipocalins	100	70	PLM∗	0.07	10.4
4	1hms	Heart muscle fatty acid-binding protein (HFABP)	Lipocalins	64	63	OLA∗	0.3	13
5	1b56	Epidermal fatty acid-binding protein (EFABP)	Lipocalins	51	62	PLM∗	0.3	6.4
6	1pmp	Myelin P2 (P2)	Lipocalins	64	61	OLI∗	0.1	12
7	1qjg	Ketosteroid isomerase	Cystatin-like	18	59	EQU	N/A	2.2
8	1hwr	HIV-1 protease	Acid proteases	15	47	216	N/A	12.5
9	2lbd	Retinoic acid receptor gamma (RAR-gamma)	Nuclear receptor ligand-binding domain	11	46	REA∗	N/A	1.6
10	1com	Chorismate mutase	Bacillus chorismate mutase-like	14	46	PRE	N/A	5.9
11	1flj	Rat (Rattus norvegicus), isozyme II	Carbonic anhydrase	10	45	GTT	N/A	5.7
12	1cqq	Human rhinovirus type 2	Trypsin-like serine proteases	14	43	AG7	N/A	17.9
13	1ftp	Locus muscle fatty acid-binding protein (L-MFABP)	Lipocalins	42	42	None∗	N/A	18.9
14	1opa	Cellular retinol-binding protein II (CRBPII)	Lipocalins	37	40	None∗	N/A	13.3
15	1ecm	Chorismate mutase domain of P-protein	Chorismate mutase 11	9	40	TSA	N/A	6.1
16	2cbr	Cellular retinoic-acid binding protein II (CRABP-II)	Lipocalins	37	37	A80∗	1.3	14.2

Marked by ∗ are ligands/binding sites known to bind/be similar to the query protein.