BSAlign: Binding Site Aligner
Zeyar Aung and
Joo Chuan Tong
Zeyar Aung and Joo Chuan Tong
Institute for Infocomm
Version 1.0 (beta) for Win32 (Windows 98, 2000, XP, Vista) (released 30-May-2008)
Detection of ligand-binding sites in protein structures is a crucial task in structural bioinformatics, and has applications in the 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 the similar sites on the other protein structures that the same ligand is likely to bind. 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 (as illustrated below). We represent protein structures and binding sites 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. Thus, the proposed BSAlign method can be an important contribution towards speed-critical applications such as drug discovery in which a large volume of proteins are needed to be processed.
Z. Aung and J.C. Tong, BSAlign: a rapid graph-based algorithm for detecting ligand-binding sites in protein structures, Genome Informatics, 21:65-76, 2008. (pdf)