FiberDock: A web server for flexible induced-fit backbone refinement in molecular docking

Efrat Mashiach, Ruth Nussinov, Haim J. Wolfson*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Protein-protein docking algorithms aim to predict the structure of a complex given the atomic structures of the proteins that assemble it. The docking procedure usually consists of two main steps: docking candidate generation and their refinement. The refinement stage aims to improve the accuracy of the candidate solutions and to identify nearnative solutions among them. During protein-protein interaction, both side chains and backbone change their conformation. Refinement methods should model these conformational changes in order to obtain a more accurate model of the complex. Handling protein backbone flexibility is a major challenge for docking methodologies, since backbone flexibility adds a huge number of degrees of freedom to the search space. FiberDock is the first docking refinement web server, which accounts for both backbone and side-chain flexibility. Given a set of up to 100 potential docking candidates, FiberDock models the backbone and side-chain movements that occur during the interaction, refines the structures and scores them according to an energy function. The FiberDock web server is free and available with no login requirementat http://bioinfo3d.cs.tau.ac.il/FiberDock/.

Original languageEnglish
Article numbergkq373
Pages (from-to)W457-W461
JournalNucleic Acids Research
Volume38
Issue numberSUPPL. 2
DOIs
StatePublished - 11 May 2010

Funding

FundersFunder number
Hermann Minkowski Minerva Geometry Center
National Institutes of HealthHHSN261200800001E
National Cancer InstituteZIABC010442
Israel Academy of Sciences and Humanities
Israel Science Foundation1403/09

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