title: G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design.
abstract: Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G-LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/.
authors.affiliation: Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047.
authors.forename: Hui Sun
authors.initials: HS
authors.lastname: Lee
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, University of Kansas, Lawrence, Kansas, 66047.
authors.forename: Wonpil
authors.initials: W
authors.lastname: Im
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D015195:Drug Design; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D064878:Web Browser
chemical_list: D011506:Proteins
keywords: computer-aided drug design; local structure comparison; molecular recognition; structural bioinformatics
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