Ligand binding: functional site location, similarity and docking

Abstract

Computational methods for the detection and characterisation of protein ligand-binding sites have increasingly become an area of interest now that large amounts of protein structural information are becoming available prior to any knowledge of protein function. There have been particularly interesting recent developments in the following areas: first, functional site detection, whereby protein evolutionary information has been used to locate binding sites on the protein surface; second, functional site similarity, whereby structural similarity and three-dimensional templates can be used to compare and classify and potentially locate new binding sites; and third, ligand docking, which is being used to find and validate functional sites, in addition to having more conventional uses in small-molecule lead discovery.