Docking of protein molecular surfaces with evolutionary trace analysis Export

@article{citeulike:2239449, 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). Proteins 2007. {\copyright} 2007 Wiley-Liss, Inc.}, address = {Japan Biological Information Research Center, Japan Biological Informatics Consortium, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan; Hitachi Software Engineering Co., Ltd, 1-1-43, Suehiro-cho, Tsurumi-Ku, Yokohama, 230-0045, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan; Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan; Structure and Function of Biomolecules, SORST, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan}, author = {Kanamori, Eiji and Murakami, Yoichi and Tsuchiya, Yuko and Standley, Daron M. and Nakamura, Haruki and Kinoshita, Kengo}, citeulike-article-id = {2239449}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/prot.21737}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17803239}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17803239}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/116312100/ABSTRACT}, doi = {10.1002/prot.21737}, issn = {1097-0134}, journal = {Proteins: Structure, Function, and Bioinformatics}, keywords = {docking-scoring-function, evolutionary-trace, modelling-interactions}, number = {4}, pages = {832--838}, posted-at = {2008-01-16 14:10:56}, priority = {2}, title = {Docking of protein molecular surfaces with evolutionary trace analysis}, url = {http://dx.doi.org/10.1002/prot.21737}, volume = {69}, year = {2007} }

TY - JOUR ID - citeulike:2239449 L3 - citeulike-article-id:2239449 N2 - 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. IS - 4 JF - Proteins: Structure, Function, and Bioinformatics SN - 1097-0134 AD - Japan Biological Information Research Center, Japan Biological Informatics Consortium, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan; Hitachi Software Engineering Co., Ltd, 1-1-43, Suehiro-cho, Tsurumi-Ku, Yokohama, 230-0045, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan; Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan; Structure and Function of Biomolecules, SORST, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan EP - 838 TI - Docking of protein molecular surfaces with evolutionary trace analysis VL - 69 SP - 832 KW - docking-scoring-function KW - evolutionary-trace KW - modelling-interactions AU - Kanamori, Eiji AU - Murakami, Yoichi AU - Tsuchiya, Yuko AU - Standley, Daron AU - Nakamura, Haruki AU - Kinoshita, Kengo PY - 2007/// UR - http://dx.doi.org/10.1002/prot.21737 ER -