Geometry-based flexible and symmetric protein docking.
We present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3-5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run-time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying C(n) symmetry for any n in a matter of minutes on a desktop PC. Most of the algorithms presented here are available at the Tel Aviv University Structural Bioinformatics Web server (http://bioinfo3d.cs.tau.ac.il/).
School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.
Dina
D
Schneidman-Duhovny
Yuval
Y
Inbar
Ruth
R
Nussinov
Haim J
HJ
Wolfson
D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D019281:Dimerization; D006801:Humans; D020407:Internet; D046911:Macromolecular Substances; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D009154:Mutation; D011487:Protein Conformation; D017510:Protein Folding; D025941:Protein Interaction Mapping / Q000379:methods*; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D055672:Static Electricity; D040681:Structural Homology, Protein
D046911:Macromolecular Substances