BSAlign: a rapid graph-based algorithm for detecting ligand-binding sites in protein structures.
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/.
Aung
Zeyar
Z
Institute for Infocomm Research, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore. azeyar@i2r.a-star.edu.sg
Tong
Joo Chuan
JC
D000225:Adenine / Q000737:chemistry; D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology; D003196:Computer Graphics; D004798:Enzymes / Q000737:chemistry / Q000235:genetics; D008024:Ligands; D008957:Models, Genetic; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D012680:Sensitivity and Specificity; D016415:Sequence Alignment
D004798:Enzymes; D008024:Ligands; D011506:Proteins; D000225:Adenine