title: 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 binding sites. Here, we present the results as a relational database Pocket Similarity Search using Multiple-sketches (PoSSuM) including all the discovered pairs with annotations of various types. PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar ones. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures, which provides important clues for characterizing protein structures with unclear functions. The PoSSuM database is freely available at http://possum.cbrc.jp/PoSSuM/.
authors.affiliation: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8568, Japan.
authors.forename: Jun-Ichi
authors.initials: J
authors.lastname: Ito
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Tabei
authors.forename: Kana
authors.initials: K
authors.lastname: Shimizu
authors.forename: Koji
authors.initials: K
authors.lastname: Tsuda
authors.forename: Kentaro
authors.initials: K
authors.lastname: Tomii
mesh_terms: D001665:Binding Sites; D030562:Databases, Protein; D015195:Drug Design; D008024:Ligands; D058977:Molecular Sequence Annotation; D011487:Protein Conformation; D014584:User-Computer Interface
chemical_list: D008024:Ligands