Dataset Information

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.

SUBMITTER: Heo L

PROVIDER: S-EPMC4086128 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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GalaxySite: ligand-binding-site prediction by using molecular docking.

Heo Lim L Shin Woong-Hee WH Lee Myeong Sup MS Seok Chaok C

Nucleic acids research 20140421 Web Server issue

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. Accordin ...[more]

PMID: 24753427

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Dataset Information

GalaxySite: ligand-binding-site prediction by using molecular docking.

Publications

GalaxySite: ligand-binding-site prediction by using molecular docking.

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