Welcome to the AutoSite Home Page

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.

Points within clusters are labeled to denote a preference for hydrophobic, or hydrogen-bond donor and acceptor ligand atoms, thus yielding a ”colored” 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.

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, Volume 32, Issue 20, 15 October 2016, Pages 3142–3149, 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.

NOTE: AutoSite is used in the AutoGridFR (AGFR) to identify binding pockets. The AFGRgui graphical user interface allows performing AutoSite calculations and visually inspect the generated clusters of points filling pockets.