HOMOLOBIND identifies residues in protein sequences with significant similarity to structurally characterized binding sites. The program predicts residues in ligand and protein binding sites with estimated true postive rates of 98% and 88%, respectively, at 1% false positive rates. Binding sites are transferred from LIGBASE and PIBASE through ASTRAL/ASTEROIDS alignments onto SUPERFAMILY domain assignments.

The current release is based on SCOP v1.73 domain classification. SUPERFAMILY has recently (Nov 2010) updated to SCOP v1.75 domain definitions, and the corresponding HOMOLOBIND update will be available by the end of 2010.

The HOMOLOBIND software package is freely available under the GPL v3 license.
The current release (v 1.1) is available for download here: homolobind_v1.1.tar.gz.
This package includes a users manual (also here) and example input files to recreate Figures 4 and 5 in the accompanying manuscript.

HOMOLOBIND results for several complete proteomes are available for download
(based on Nov 1, 2009 SUPERFAMILY release):

species
Homo sapiens	hs.homolobind.out.gz (55 MB)
Mus musculus	mm.homolobind.out.gz (50 MB)
Drosophila melanogaster	dm.homolobind.out.gz (25 MB)
Caenorhabditis elegans	ce.homolobind.out.gz (20 MB)
Saccharomyces cerevisiae	sc.homolobind.out.gz (6 MB)
Escherichia coli	ec.homolobind.out.gz (3 MB)
NCBI viral sequence set	vl.homolobind.out.gz (14 MB)

Proteome-wide prediction of overlapping protein and ligand binding sites using structure.
Davis FP, Molecular BioSystems, 2011. Advance Article. doi:10.1039/C0MB00200C (reprint)

HOMOLOBIND uses data from the following sources:

• ASTRAL/ASTEROIDS: Chandonia, et al. Nucleic Acids Res (2004) 32:D189-92.
• LIGBASE: Stuart, et al. Bioinformatics (2002) 8(1):200-1.
• PIBASE: Davis and Sali. Bioinformatics (2005) 21(9):1901-7.
• SCOP: Murzin, et al. J Mol Biol (1995) 247(4):536-40.
• SUPERFAMILY: Wilson, et al. Nucleic Acids Res (2009) 37:D380-6.