Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities.

ABSTRACT:

Background

The identification of ligand binding sites is a key task in the annotation of proteins with known structure but uncharacterized function. Here we describe a knowledge-based method exploiting the observation that unrelated binding sites share small structural motifs that bind the same chemical fragments irrespective of the nature of the ligand as a whole.

Results

PDBinder compares a query protein against a library of binding and non-binding protein surface regions derived from the PDB. The results of the comparison are used to derive a propensity value for each residue which is correlated with the likelihood that the residue is part of a ligand binding site. The method was applied to two different problems: i) the prediction of ligand binding residues and ii) the i

SUBMITTER: Bianchi V 

PROVIDER: S-EPMC3434446 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature