PoSSuM: Pocket Similarity Search using Multiple-Sketches
|National Institute of Advanced Industrial Science and Technology|
|This site contains a database of protein-ligand binding sites that have been compared and numbered according to resemblance in structure.|
Comparing the huge amounts of small molecule binding sites of proteins available in the PDB (Protein Data Bank) is important in order to determine anticipated protein functions, the knowledge of which may then be applied in the research and discovery of new drugs.
The software program used, "SketchSort", proved to be an extremely fast method. All-pair similarity searches were done for 3.4 million binding sites and over 24 million analogous pairs were found.
The results, presented as a PoSSuM (Pocket Similarity Search using Multiple-Sketches) database contain all pairs identified and include commentary notes of various types, namely CATH (protein structure classification according to Class, Architecture, Topology and Homologous superfamily), SCOP (Structural Classification of Proteins), EC number (Enzyme Commission number) and gene ontology.
Two search modes are provided:
Search K, to find analogous binding sites to a familiar ligand-binding site entered and Search P, to predict ligands that show potential to bind to a protein structure entered.