title: GalaxySite: ligand-binding-site prediction by using molecular docking.
abstract: Knowledge of ligand-binding sites of proteins provides invaluable information for functional studies, drug design and protein design. Recent progress in ligand-binding-site prediction methods has demonstrated that using information from similar proteins of known structures can improve predictions. The GalaxySite web server, freely accessible at http://galaxy.seoklab.org/site, combines such information with molecular docking for more precise binding-site prediction for non-metal ligands. According to the recent critical assessments of structure prediction methods held in 2010 and 2012, this server was found to be superior or comparable to other state-of-the-art programs in the category of ligand-binding-site prediction. A strong merit of the GalaxySite program is that it provides additional predictions on binding ligands and their binding poses in terms of the optimized 3D coordinates of the protein-ligand complexes, whereas other methods predict only identities of binding-site residues or copy binding geometry from similar proteins. The additional information on the specific binding geometry would be very useful for applications in functional studies and computer-aided drug discovery.
authors.affiliation: Department of Chemistry, Seoul National University, Seoul 151-747, Korea.
authors.forename: Lim
authors.initials: L
authors.lastname: Heo
authors.affiliation: Department of Chemistry, Seoul National University, Seoul 151-747, Korea.
authors.forename: Woong-Hee
authors.initials: WH
authors.lastname: Shin
authors.affiliation: Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul 138-736, Korea chaok@snu.ac.kr.
authors.forename: Myeong Sup
authors.initials: MS
authors.lastname: Lee
authors.affiliation: Department of Chemistry, Seoul National University, Seoul 151-747, Korea chaok@snu.ac.kr.
authors.forename: Chaok
authors.initials: C
authors.lastname: Seok
mesh_terms: D001665:Binding Sites; D020407:Internet; D008024:Ligands; D062105:Molecular Docking Simulation / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins
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