Docking of protein molecular surfaces with evolutionary trace analysis

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

研究成果: Article査読

24 被引用数 (Scopus)

抄録

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).

本文言語English
ページ(範囲)832-838
ページ数7
ジャーナルProteins: Structure, Function and Genetics
69
4
DOI
出版ステータスPublished - 2007 12 1
外部発表はい

ASJC Scopus subject areas

  • 構造生物学
  • 生化学
  • 分子生物学

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