Protein‐binding site prediction based on three‐dimensional protein modeling

Structural information of a protein can guide one to understand the function of the protein, and ligand binding is one of the major biochemical functions of proteins. We have applied a two‐stage template‐based ligand binding site prediction method to CASP8 targets and achieved high quality results with accuracy/coverage = 70/80 (LEE). First, templates are used for protein structure modeling and then for binding site prediction by structural clustering of ligand‐containing templates to the predicted protein model. Remarkably, the results are only a few percent worse than those one can obtain from native structures, which were available only after the prediction. Prediction was performed without knowing identity of ligands, and consequently, in many cases the ligand molecules used for prediction were different from the actual ligands, and yet we find that the prediction was quite successful. The current approach can be easily combined with experiments to investigate protein activities in a systematic way. Proteins 2009. © 2009 Wiley‐Liss, Inc.