title: Docking of protein molecular surfaces with evolutionary trace analysis.
abstract: 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).
authors.affiliation: Japan Biological Information Research Center, Japan Biological Informatics Consortium, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan.
authors.forename: Eiji
authors.initials: E
authors.lastname: Kanamori
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Murakami
authors.forename: Yuko
authors.initials: Y
authors.lastname: Tsuchiya
authors.forename: Daron M
authors.initials: DM
authors.lastname: Standley
authors.forename: Haruki
authors.initials: H
authors.lastname: Nakamura
authors.forename: Kengo
authors.initials: K
authors.lastname: Kinoshita
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods; D030562:Databases, Protein; D019281:Dimerization; D019143:Evolution, Molecular; D021621:Imaging, Three-Dimensional; D009010:Monte Carlo Method; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software