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.
Highlights
Proteins perform their biochemical functions by interacting with other biomolecules such as small ligands, other proteins or nucleic acids
Methods that use experimental structures of similar protein–ligand complexes have been successfully applied in binding-site predictions in critical assessment of structure prediction (CASP) experiments [4,5,6,7]
These methods predict only ligand-binding residues or ligandbinding geometry based on simple structure superimposition to similar protein–ligand complexes [8,9,10,11,12]
Summary
Proteins perform their biochemical functions by interacting with other biomolecules such as small ligands, other proteins or nucleic acids. In such methods, binding-site information of homologous proteins of known structures is utilized by assuming that similar protein–ligand contacts occur in the target protein These methods predict only ligand-binding residues or ligandbinding geometry based on simple structure superimposition to similar protein–ligand complexes [8,9,10,11,12]. The binding geometry obtained by docking can be different from the geometry obtained by simple structure superimposition with similar proteins, and the binding pose optimized by docking tends to have physically more realistic geometry with no severe steric clashes Such precise information would be very useful for the prediction of specific functions and applications in drug discovery. The performance of GalaxySite was superior or comparable to other state-of-the-art prediction methods
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