{"id":14,"date":"2018-12-14T00:43:17","date_gmt":"2018-12-14T00:43:17","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/ccsb-3\/?page_id=14"},"modified":"2021-10-26T18:29:18","modified_gmt":"2021-10-26T18:29:18","slug":"autodock-crankpep","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/autosite\/","title":{"rendered":"Homepage"},"content":{"rendered":"

AutoSite<\/h3><\/h1><\/div>

Welcome to the AutoSite Home Page<\/h1>\n

AutoSite is a computational method for identifying and characterizing binding sites in macro-molecules with a known three-dimensional structure (receptor). Binding sites are identified by clustering of high affinity points. These clusters of points correspond to potential binding pockets.<\/p>\n

Points within clusters are labeled to denote a preference for hydrophobic, or hydrogen-bond donor and acceptor ligand atoms, thus yielding a \u201dcolored\u201d description of the binding pocket. These colored-points are used to derives a set of putative positions for hydrophobic, and hydrogen-bond forming ligand atoms called feature points.<\/p>\n

The method has been demonstrated to outperform state-of-the-art energy- and geometry-based approaches in identifying binding-sites of known ligands as published in Bioinformatics<\/em>, Volume 32, Issue 20, 15 October 2016, Pages 3142\u20133149,\u00a0https:\/\/doi.org\/10.1093\/bioinformatics\/btw367.<\/a> In this paper we demonstrate that our method places feature points of the proper type within 2.0 Angstroms of 79% of hydrophobic ligand atoms, 81% hydrogen-bond acceptor ligand atoms involved in a hydrogen bond with the receptor, and 63% of hydrogen atoms forming hydrogen bonds with the receptor for the set of 85 ligands from the Astex Diverse Set.<\/p>\n

NOTE<\/strong>: AutoSite is used in the AutoGridFR (AGFR) to identify binding pockets. The AFGRgui<\/a> graphical user interface allows performing AutoSite calculations and visually inspect the generated clusters of points filling pockets.<\/p>\n<\/div>

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