ProBiS-Dock Database: A Web Server and Interactive Web Repository of Small Ligand-Protein Binding Sites for Drug Design

Abstract

We have developed a new system, ProBiS-Dock, which can be used to determine the different types of protein binding sites for small ligands. The binding sites identified this way are then used to construct a new binding site database, the ProBiS-Dock Database, that allows for the ranking of binding sites according to their utility for drug development. The newly constructed database currently has more than 1.4 million binding sites and offers the possibility to investigate potential drug targets originating from different biological species. The interactive ProBiS-Dock Database, a web server and repository that consists of all small-molecule ligand binding sites in all of the protein structures in the Protein Data Bank, is freely available at http://probis-dock-database.insilab.org. The ProBiS-Dock Database will be regularly updated to keep pace with the growth of the Protein Data Bank, and our anticipation is that it will be useful in drug discovery.