TY - JOUR
T1 - Principles of flexible protein-protein docking
AU - Andrusier, Nelly
AU - Mashiach, Efrat
AU - Nussinov, Ruth
AU - Wolfson, Haim J.
PY - 2008/11/1
Y1 - 2008/11/1
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.
AB - 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.
KW - Backbone flexibility
KW - Flexible docking
KW - Modeling protein-protein docking
KW - Rigid-body optimization
KW - Side-chain refinement
UR - http://www.scopus.com/inward/record.url?scp=52249122794&partnerID=8YFLogxK
U2 - 10.1002/prot.22170
DO - 10.1002/prot.22170
M3 - ???researchoutput.researchoutputtypes.contributiontojournal.systematicreview???
C2 - 18655061
AN - SCOPUS:52249122794
SN - 0887-3585
VL - 73
SP - 271
EP - 289
JO - Proteins: Structure, Function and Genetics
JF - Proteins: Structure, Function and Genetics
IS - 2
ER -