Exhaustive comparison and classification of ligand-binding surfaces in proteins

Yoichi Murakami, Kengo Kinoshita, Akira R. Kinjo, Haruki Nakamura

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)


Many proteins function by interacting with other small molecules (ligands). Identification of ligand-binding sites (LBS) in proteins can therefore help to infer their molecular functions. A comprehensive comparison among local structures of LBSs was previously performed, in order to understand their relationships and to classify their structural motifs. However, similar exhaustive comparison among local surfaces of LBSs (patches) has never been performed, due to computational complexity. To enhance our understanding of LBSs, it is worth performing such comparisons among patches and classifying them based on similarities of their surface configurations and electrostatic potentials. In this study, we first developed a rapid method to compare two patches. We then clustered patches corresponding to the same PDB chemical component identifier for a ligand, and selected a representative patch from each cluster. We subsequently exhaustively as compared the representative patches and clustered them using similarity score, PatSim. Finally, the resultant PatSim scores were compared with similarities of atomic structures of the LBSs and those of the ligand-binding protein sequences and functions. Consequently, we classified the patches into 2000 well-characterized clusters. We found that about 63% of these clusters are used in identical protein folds, although about 25% of the clusters are conserved in distantly related proteins and even in proteins with cross-fold similarity. Furthermore, we showed that patches with higher PatSim score have potential to be involved in similar biological processes.

Original languageEnglish
Pages (from-to)1379-1391
Number of pages13
JournalProtein Science
Issue number10
Publication statusPublished - 2013 Oct


  • Electrostatics potentials
  • Exhaustive comparison
  • Ligand-binding site
  • Molecular surfaces
  • Protein-ligand interactions

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology


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