Premium
Docking of protein molecular surfaces with evolutionary trace analysis
Author(s) -
Kanamori Eiji,
Murakami Yoichi,
Tsuchiya Yuko,
Standley Daron M.,
Nakamura Haruki,
Kinoshita Kengo
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21737
Subject(s) - complementarity (molecular biology) , docking (animal) , monte carlo method , biological system , evolutionary algorithm , computer science , computational biology , algorithm , chemistry , biology , mathematics , artificial intelligence , genetics , statistics , medicine , nursing
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). Proteins 2007. © 2007 Wiley‐Liss, Inc.