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URL: http://possum.cbrc.jp/PoSSuM/
Proper Citation: PoSSuM (RRID:SCR_006109)
Description: Relational database of all the discovered similar pairs in a huge number of protein-ligand binding sites with annotations of various types (e.g., CATH, SCOP, EC number, Gene ontology). They used a tremendously fast algorithm called SketchSort that enables the enumeration of similar pairs in a huge number of protein-ligand binding sites. They 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. 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: # 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. # 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.
Abbreviations: PoSSuM
Synonyms: PoSSuM - POcket Similarity Search Using Multiple-Sketches, Pocket Similarity Search using Multiple-Sketches (PoSSuM), PoSSuM Database, POcket Similarity Search Using Multiple-Sketches
Resource Type: data or information resource, database
Defining Citation: PMID:22135290, PMID:22113700
Keywords: binding site, ligand-binding site, protein function, protein, prediction, small molecule, drug discovery
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Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
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National Institute of Advanced Industrial Science and Technology |
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