LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.

ABSTRACT:

Background

Identifying pockets on protein surfaces is of great importance for many structure-based drug design applications and protein-ligand docking algorithms. Over the last ten years, many geometric methods for the prediction of ligand-binding sites have been developed.

Results

We present LIGSITEcsc, an extension and implementation of the LIGSITE algorithm. LIGSITEcsc is based on the notion of surface-solvent-surface events and the degree of conservation of the involved surface residues. We compare our algorithm to four other approaches, LIGSITE, CAST, PASS, and SURFNET, and evaluate all on a dataset of 48 unbound/bound structures and 210 bound-structures. LIGSITEcsc performs slightly better than the other tools and achieves a success rate of 71% and 75%, respectively.

SUBMITTER: Huang B 

PROVIDER: S-EPMC1601958 | biostudies-literature | 2006 Sep

REPOSITORIES: biostudies-literature