PoSSuM: a database of similar protein-ligand binding and putative pockets.

ABSTRACT: Numerous potential ligand-binding sites are available today, along with hundreds of thousands of known binding sites observed in the PDB. Exhaustive similarity search for such vastly numerous binding site pairs is useful to predict protein functions and to enable rapid screening of target proteins for drug design. Existing databases of ligand-binding sites offer databases of limited scale. For example, SitesBase covers only ~33,000 known binding sites. Inferring protein function and drug discovery purposes, however, demands a much more comprehensive database including known and putative-binding sites. Using a novel algorithm, we conducted a large-scale all-pairs similarity search for 1.8 million known and potential binding sites in the PDB, and discovered over 14 million similar pairs of b

SUBMITTER: Ito J 

PROVIDER: S-EPMC3245044 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature