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

By Efrat Mashiach, Dina Schneidman-Duhovny, Nelly Andrusier, Ruth Nussinov, Haim J. Wolfson. Nucleic Acids Res., 2008

743 citations recorded by the source corpus.

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/.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cfd652ca5edb0313e2b6ae7dbeb40f2dad2feca5

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. M. V. van Dijk
2. Sjoerd Jacob de Vries
3. Alexandre M. J. J. Bonvin
4. Alessandro Sette
5. Bjoern Peters
6. D. Lloyd Evans
7. S. Joshi
8. Pierre Tufféry

In Materials Chemistry

1. Alexandre M. J. J. Bonvin
2. M. V. van Dijk
3. Sjoerd Jacob de Vries
4. D. Lloyd Evans
5. Julien Rey
6. S. Joshi
7. Pierre Tufféry
8. S. D. de Vries

In Molecular Biology

1. Alexandre M. J. J. Bonvin
2. M. V. van Dijk
3. Alessandro Sette
4. Bjoern Peters
5. Sinu Paul
6. Swapnil Mahajan
7. Sandeep Kumar Dhanda
8. Ward Fleri

Citations in the corpus

• Elucidating modes of activation and herbicide resistance by sequence assembly and molecular modelling of the Acetolactate synthase complex in sugarcane. (2016, methodology): “After processing with PatchDock, FireDock and FibreDock a total of 53 models (31 from the VAT1 domain 1 and 22 from the VAT1 domain 2 runs) were obtained.”
• InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs (2018, background): “Many template-free docking servers implement a rigid-body docking approach, sometimes followed by rescoring: PatchDock (9), FireDock (10), HexServer (11), ZDOCK (12), FRODOCK 2.”
• The HADDOCK web server for data-driven biomolecular docking (2010, methodology): “Among those, only PatchDock/FireDock and the RosettaDock server can deal with structural flexibility but only at the side chain level.”
• The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design (2017, methodology): “Users can improve the solutions using the FireDock (78, 79) link at the bottom of the page.”