Detailed overview:
PoSSuM - Pocket Similarity Search using Multi-Sketches
Title: PoSSuM - Pocket Similarity Search using Multi-Sketches
Title abbreviated: PoSSuM
Creator: Universität <Tokyo>; CBRC = Computational Biology Research Center
Abstract: Today, vast amounts of protein-small molecule binding sites can be found in the Protein Data Bank (PDB). Exhaustive comparison of them is computationally demanding, but useful in the prediction of protein functions and drug discovery. We proposed a tremendously fast algorithm called "SketchSort" that enables the enumeration of similar pairs in a huge number of protein-ligand binding sites. We conducted all-pair similarity searches for 3.4 million known and potential binding sites using the proposed method and discovered over 24 million similar pairs of binding sites. We present the results as a relational database Pocket Similarity Search using Multiple-Sketches (PoSSuM), which includes all the discovered pairs with annotations of various types (e.g., CATH, SCOP, EC number, Gene ontology). 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. Basically, the users can search similar binding pockets using two search modes: i) "Search K" is useful for finding similar binding sites for a known ligand-binding site. Post a known ligand-binding site (a pair of "PDB ID" and "HET code") in the PDB, and PoSSuM will search similar sites for the query site; ii) "Search P" is useful for predicting ligands that potentially bind to a structure of interest. Post a known protein structure (PDB ID) in the PDB, and PoSSuM will search similar known-ligand binding sites for the query structure. [Information of the supplier]
Subject: General topics of biochemistry (572.3)
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Audience: Intermediate; Experts
Language: English
Format: website; database
Resource type: Factual databases
Access: free
Metadata update date: 2012-10-31
Metadata provider: UBFfm
URL of this vifabio-resource:
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