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Genome Informatics 15(2): 3141 (2004) 31 Comprehensive Identification of "Druggable" Protein

Summary: Genome Informatics 15(2): 3141 (2004) 31
Comprehensive Identification of "Druggable" Protein
Ligand Binding Sites
Jianghong An1 Maxim Totrov2 Ruben Abagyan1
jianghon@scripps.edu max@molsoft.com abagyan@scripps.edu
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037,
Molsoft,LLC, La Jolla, CA 92037, USA
We have developed a new computational algorithm for de novo identification of protein-ligand
binding pockets and performed a large-scale validation of the algorithm on two systematically
collected datasets from all crystallographic structures in the Protein Data Bank (PDB). This al-
gorithm, called DrugSite, takes a three-dimensional protein structure as input and returns the
location, volume and shape of the putative small molecule binding sites by using a physical po-
tential and without any knowledge about a potential ligand molecule. We validated this method
using 17,126 binding sites from complexes and apo-structures from the PDB. Out of 5,616 bind-
ing sites from protein-ligand complexes, 98.8% were identified by predicted pockets. In proteins
having known binding sites, 80.9% were predicted by the largest predicted pocket and 92.7% by
the first two. The average ratio of predicted contact area to the total surface area of the protein


Source: Abagyan, Ruben - School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego


Collections: Biology and Medicine