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Pocketome via Comprehensive Identification and Classification of Ligand Binding

Summary: Pocketome via Comprehensive Identification
and Classification of Ligand Binding
Jianghong An, Maxim Totrov§, and Ruben Abagyan¶
We developed a new computational algorithm for the ac-
curate identification of ligand binding envelopes rather
than surface binding sites. We performed a large scale
classification of the identified envelopes according to
their shape and physicochemical properties. The predict-
ing algorithm, called PocketFinder, uses a transformation
of the Lennard-Jones potential calculated from a three-
dimensional protein structure and does not require any
knowledge about a potential ligand molecule. We vali-
dated this algorithm using two systematically collected
data sets of ligand binding pockets from complexed
(bound) and uncomplexed (apo) structures from the Pro-
tein Data Bank, 5616 and 11,510, respectively. As many as
96.8% of experimental binding sites were predicted at
better than 50% overlap level. Furthermore 95.0% of the
asserted sites from the apo receptors were predicted at


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


Collections: Biology and Medicine