Docking of protein molecular surfaces with evolutionary trace analysis

Eiji Kanamori, Yoichi Murakami, Yuko Tsuchiya, Daron M. Standley, Haruki Nakamura, Kengo Kinoshita

Research output: Contribution to journalArticlepeer-review

26 Citations (Scopus)


We have developed a new method to predict protein-protein complexes based on the shape complementarity of the molecular surfaces, along with sequence conservation obtained by evolutionary trace (ET) analysis. The docking is achieved by optimization of an object function that evaluates the degree of shape complementarity weighted by the conservation of the interacting residues. The optimization is carried out using a genetic algorithm in combination with Monte Carlo sampling. We applied this method to CAPRI targets and evaluated the performance systematically. Consequently, our method could achieve native-like predictions in several cases. In addition, we have analyzed the feasibility of the ET method for docking simulations, and found that the conservation information was useful only in a limited category of proteins (signal related proteins and enzymes).

Original languageEnglish
Pages (from-to)832-838
Number of pages7
JournalProteins: Structure, Function and Genetics
Issue number4
Publication statusPublished - 2007 Dec
Externally publishedYes


  • 3D structure
  • Computational biology
  • Prediction of protein complex
  • Protein-protein interaction
  • Shape complementarity

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology


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