Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures.
This article describes a new method for predicting ligand-binding sites of proteins. The method involves calculating the van der Waals interaction energy between a protein and probes placed on the protein surface, and then clustering the probes with attractive interaction to find the energetically most favorable locus. In 80% (28/35) of the test cases, the ligand-binding site was successfully predicted on a ligand-bound protein structure, and in 77% (27/35) was successfully predicted on an unbound structure. Our method was used to successfully predict ligand-binding sites unaffected by induced-fit as long as its scales were not very large, and it contributed to a significant improvement in prediction with unbound state protein structures. This represents a significant advance over conventional methods in detecting ligand-binding sites on uncharacterized proteins. Moreover, our method can predict ligand-binding sites with a narrower locus than those achieved using conventional methods.
Morita
Mizuki
M
Department of Biotechnology, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan. mizuki@bi.a.u-tokyo.ac.jp
Nakamura
Shugo
S
Shimizu
Kentaro
K
D001059:Apoproteins / Q000737:chemistry*; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D008024:Ligands; D020539:Sequence Analysis, Protein
D001059:Apoproteins; D008024:Ligands