EMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.

ABSTRACT: Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-sca

SUBMITTER: Brylinski M 

PROVIDER: S-EPMC4168975 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature