FireDock: a web server for fast interaction refinement in molecular docking.

Efrat Mashiach; Dina Schneidman-Duhovny; Nelly Andrusier; Ruth Nussinov; Haim J. Wolfson

doi:10.1093/nar/gkn186

FireDock: a web server for fast interaction refinement in molecular docking.

Efrat Mashiach^*, Dina Schneidman-Duhovny, Nelly Andrusier, Ruth Nussinov, Haim J. Wolfson

^*Corresponding author for this work

Tel Aviv University

Research output: Contribution to journal › Article › peer-review

612 Scopus citations

Abstract

Structural details of protein-protein interactions are invaluable for understanding and deciphering biological mechanisms. Computational docking methods aim to predict the structure of a protein-protein complex given the structures of its single components. Protein flexibility and the absence of robust scoring functions pose a great challenge in the docking field. Due to these difficulties most of the docking methods involve a two-tier approach: coarse global search for feasible orientations that treats proteins as rigid bodies, followed by an accurate refinement stage that aims to introduce flexibility into the process. The FireDock web server, presented here, is the first web server for flexible refinement and scoring of protein-protein docking solutions. It includes optimization of side-chain conformations and rigid-body orientation and allows a high-throughput refinement. The server provides a user-friendly interface and a 3D visualization of the results. A docking protocol consisting of a global search by PatchDock and a refinement by FireDock was extensively tested. The protocol was successful in refining and scoring docking solution candidates for cases taken from docking benchmarks. We provide an option for using this protocol by automatic redirection of PatchDock candidate solutions to the FireDock web server for refinement. The FireDock web server is available at http://bioinfo3d.cs.tau.ac.il/FireDock/.

Original language	English
Pages (from-to)	W229-232
Journal	Nucleic Acids Research
Volume	36
Issue number	Web Server issue
DOIs	https://doi.org/10.1093/nar/gkn186
State	Published - 1 Jul 2008

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title = "FireDock: a web server for fast interaction refinement in molecular docking.",

abstract = "Structural details of protein-protein interactions are invaluable for understanding and deciphering biological mechanisms. Computational docking methods aim to predict the structure of a protein-protein complex given the structures of its single components. Protein flexibility and the absence of robust scoring functions pose a great challenge in the docking field. Due to these difficulties most of the docking methods involve a two-tier approach: coarse global search for feasible orientations that treats proteins as rigid bodies, followed by an accurate refinement stage that aims to introduce flexibility into the process. The FireDock web server, presented here, is the first web server for flexible refinement and scoring of protein-protein docking solutions. It includes optimization of side-chain conformations and rigid-body orientation and allows a high-throughput refinement. The server provides a user-friendly interface and a 3D visualization of the results. A docking protocol consisting of a global search by PatchDock and a refinement by FireDock was extensively tested. The protocol was successful in refining and scoring docking solution candidates for cases taken from docking benchmarks. We provide an option for using this protocol by automatic redirection of PatchDock candidate solutions to the FireDock web server for refinement. The FireDock web server is available at http://bioinfo3d.cs.tau.ac.il/FireDock/.",

author = "Efrat Mashiach and Dina Schneidman-Duhovny and Nelly Andrusier and Ruth Nussinov and Wolfson, {Haim J.}",

note = "Funding Information: We thank Oranit Dror for the helpful comments. E.M. was supported in part by a fellowship from the Edmond J. Safra Bioinformatics Program at Tel-Aviv university. The research of H.J.W has been supported in part by the Israel Science Foundation (grant no. 281/05) and by the Hermann Minkowski-Minerva Center for Geometry at TAU. The research of HJW and RN has also been supported in part by the NIAID, NIH (grant No. 1UC1AI067231) and by the Binational US-Israel Science Foundation (BSF). This project has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under contract number NO1-CO-12400. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products or organizations imply endorsement by the U.S. Government. This research was supported (in part) by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research. Funding to pay the Open Access publication charges for this article was provided by NCI contract N01-CO-12400.",

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FireDock: a web server for fast interaction refinement in molecular docking.

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