Comparative assessment of strategies to identify similar ligand-binding pockets in proteins.

ABSTRACT:

Background

Detecting similar ligand-binding sites in globally unrelated proteins has a wide range of applications in modern drug discovery, including drug repurposing, the prediction of side effects, and drug-target interactions. Although a number of techniques to compare binding pockets have been developed, this problem still poses significant challenges.

Results

We evaluate the performance of three algorithms to calculate similarities between ligand-binding sites, APoc, SiteEngine, and G-LoSA. Our assessment considers not only the capabilities to identify similar pockets and to construct accurate local alignments, but also the dependence of these alignments on the sequence order. We point out certain drawbacks of previously compiled datasets, such as the inclusion of struc

SUBMITTER: Govindaraj RG 

PROVIDER: S-EPMC5845264 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature