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PubMed · 15981269

Geometry-based flexible and symmetric protein docking.

Dina Schneidman-Duhovny·Yuval Inbar·Ruth Nussinov·Haim J Wolfson
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Abstract

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/).

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AlgorithmsAnimalsComputational BiologyComputer SimulationDatabases, ProteinDimerizationHumansInternetMacromolecular SubstancesModels, MolecularModels, StatisticalMolecular ConformationMutationProtein ConformationProtein FoldingProtein Interaction MappingProtein Structure, TertiaryProteomicsReproducibility of ResultsSoftwareStatic ElectricityStructural Homology, ProteinJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

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Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J Wolfson. 2005-08-01. Geometry-based flexible and symmetric protein docking.. https://doi.org/10.1002/prot.20562

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