Principles of flexible protein-protein docking Export

@article{citeulike:3272777, abstract = {Treating flexibility in molecular docking is a major challenge in cell biology research. Here we describe the background and the principles of existing flexible protein-protein docking methods, focusing on the algorithms and their rational. We describe how protein flexibility is treated in different stages of the docking process: in the preprocessing stage, rigid and flexible parts are identified and their possible conformations are modeled. This preprocessing provides information for the subsequent docking and refinement stages. In the docking stage, an ensemble of pre-generated conformations or the identified rigid domains may be docked separately. In the refinement stage, small-scale movements of the backbone and side-chains are modeled and the binding orientation is improved by rigid-body adjustments. For clarity of presentation, we divide the different methods into categories. This should allow the reader to focus on the most suitable method for a particular docking problem. Proteins 2008. Published Wiley-Liss, Inc.}, address = {School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel; Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program NCI - Frederick, Frederick, Maryland 21702; Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel}, author = {Andrusier, Nelly and Mashiach, Efrat and Nussinov, Ruth and Wolfson, Haim J.}, citeulike-article-id = {3272777}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/prot.22170}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18655061}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18655061}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/120847027/ABSTRACT}, doi = {10.1002/prot.22170}, journal = {Proteins: Structure, Function, and Bioinformatics}, keywords = {docking, flexibility, review}, number = {2}, pages = {271--289}, posted-at = {2008-09-16 12:33:50}, priority = {2}, title = {Principles of flexible protein-protein docking}, url = {http://dx.doi.org/10.1002/prot.22170}, volume = {73}, year = {2008} }

TY - JOUR ID - citeulike:3272777 L3 - citeulike-article-id:3272777 N2 - Treating flexibility in molecular docking is a major challenge in cell biology research. Here we describe the background and the principles of existing flexible protein-protein docking methods, focusing on the algorithms and their rational. We describe how protein flexibility is treated in different stages of the docking process: in the preprocessing stage, rigid and flexible parts are identified and their possible conformations are modeled. This preprocessing provides information for the subsequent docking and refinement stages. In the docking stage, an ensemble of pre-generated conformations or the identified rigid domains may be docked separately. In the refinement stage, small-scale movements of the backbone and side-chains are modeled and the binding orientation is improved by rigid-body adjustments. For clarity of presentation, we divide the different methods into categories. This should allow the reader to focus on the most suitable method for a particular docking problem. Proteins 2008. Published Wiley-Liss, Inc. IS - 2 JF - Proteins: Structure, Function, and Bioinformatics AD - School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel; Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program NCI - Frederick, Frederick, Maryland 21702; Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel EP - 289 TI - Principles of flexible protein-protein docking VL - 73 SP - 271 KW - docking KW - flexibility KW - review AU - Andrusier, Nelly AU - Mashiach, Efrat AU - Nussinov, Ruth AU - Wolfson, Haim PY - 2008/// UR - http://dx.doi.org/10.1002/prot.22170 ER -