BSAlign: a rapid graph-based algorithm for detecting ligand-binding sites in protein structures.

Abstract

Detection of ligand-binding sites in protein structures is a crucial task in structural bioinformatics, and has applications in important areas like drug discovery. Given the knowledge of the site in a particular protein structure that binds to a specific ligand, we can search for similar sites in the other protein structures that the same ligand is likely to bind. In this paper, we propose a new method named "BSAlign" (Binding Site Aligner) for rapid detection of potential binding site(s) in the target protein(s) that is/are similar to the query protein's ligand-binding site. We represent both the binding site and the protein structure as graphs, and employ a subgraph isomorphism algorithm to detect the similarities of the binding sites in a very time-efficient manner. Preliminary experimental results show that the proposed BSAlign binding site detection method is about 14 times faster than a well-known method called SiteEngine, while offering the same level of accuracy. Both BSAlign and SiteEngine achieve 60% search accuracy in finding adenine-binding sites from a data set of 126 proteins. The proposed method can be a useful contribution towards speed-critical applications such as drug discovery in which a large number of proteins are needed to be processed. The program is available for download at: http://www1.i2r.a-star.edu.sg/~azeyar/BSAlign/.