Geometry-based flexible and symmetric protein docking

Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

182 Scopus citations

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.

Original languageEnglish
Pages (from-to)224-231
Number of pages8
JournalProteins: Structure, Function and Genetics
Volume60
Issue number2
DOIs
StatePublished - 1 Aug 2005

Funding

FundersFunder number
National Cancer InstituteZ01BC010442

    Keywords

    • CAPRI
    • FlexDock
    • Flexible docking
    • Patchdock
    • SymmDock
    • Symmetric docking
    • Unbound docking

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