Development of a protein-ligand-binding site prediction method based on interaction energy and sequence conservation.

ABSTRACT: We present a new method for predicting protein-ligand-binding sites based on protein three-dimensional structure and amino acid conservation. This method involves calculation of the van der Waals interaction energy between a protein and many probes placed on the protein surface and subsequent clustering of the probes with low interaction energies to identify the most energetically favorable locus. In addition, it uses amino acid conservation among homologous proteins. Ligand-binding sites were predicted by combining the interaction energy and the amino acid conservation score. The performance of our prediction method was evaluated using a non-redundant dataset of 348 ligand-bound and ligand-unbound protein structure pairs, constructed by filtering entries in a ligand-binding site structure

SUBMITTER: Tsujikawa H 

PROVIDER: S-EPMC5002282 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature