Automatic prediction of protein interactions with large scale motion.
Proteins often change their conformation upon binding to other molecules. Taking these conformational changes into account in docking is an extremely difficult task: the larger the scale of the motion the harder it is to predict the structure of the association complex. Here, we present a fully automated method for flexible docking with large scale motion in one of the docked molecules. The method automatically identifies hinge regions and rigid parts and then docks the input molecules while explicitly considering the hinges and possible protein motions.
Schneidman-Duhovny
Dina
D
School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel. duhovka@post.tau.ac.il
Nussinov
Ruth
R
Wolfson
Haim J
HJ
D000465:Algorithms; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D023281:Genomics; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software
D008024:Ligands; D011506:Proteins