Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures

Mizuki Morita, Shugo Nakamura, Kentaro Shimizu

Research output: Contribution to journalArticlepeer-review

37 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)468-479
Number of pages12
JournalProteins: Structure, Function and Genetics
Issue number2
Publication statusPublished - Nov 1 2008
Externally publishedYes


  • Binding pocket
  • Conformational change
  • Energy-based method
  • Induced fit
  • Molecular recognition
  • Protein-ligand interaction
  • Substrate
  • Van der Waals interaction energy

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology


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