HOMOLOBIND

What is HOMOLOBIND

HOMOLOBIND identifies residues in protein sequences with significant similarity to structurally characterized binding sites. It transfers binding sites from LIGBASE (http://salilab.org/ligbase) and PIBASE (http://fredpdavis.com/pibase) through ASTRAL/ASTEROIDS (http://astral.berkeley.edu) alignments onto SUPERFAMILY (http://supfam.org) domain assignments.

The homology transfer procedure predicts residues in ligand and protein binding sites with estimated true positive rates of 98% and 88%, respectively, at 1% false positive rates.

This release is based on the SCOP v1.73 domain classification.

NOTE: HOMOLOBIND is maintained here for archiving purposes. The databases that HOMOLOBIND depends on have dramatically changed or stopped development.

HOMOLOBIND predictions for several species are archived at Zenodo: https://zenodo.org/record/29597

Citing HOMOLOBIND

Proteome-wide prediction of overlapping protein and ligand binding sites using structure.
Davis FP. Molecular Biosystems (2011) 7: 545-557.
http://dx.doi.org/10.1039/C0MB00200C

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.