rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids.
Identification of chemical compounds with specific biological activities is an important step in both chemical biology and drug discovery. When the structure of the intended target is available, one approach is to use molecular docking programs to assess the chemical complementarity of small molecules with the target; such calculations provide a qualitative measure of affinity that can be used in virtual screening (VS) to rank order a list of compounds according to their potential to be active. rDock is a molecular docking program developed at Vernalis for high-throughput VS (HTVS) applications. Evolved from RiboDock, the program can be used against proteins and nucleic acids, is designed to be computationally very efficient and allows the user to incorporate additional constraints and information as a bias to guide docking. This article provides an overview of the program structure and features and compares rDock to two reference programs, AutoDock Vina (open source) and Schrödinger's Glide (commercial). In terms of computational speed for VS, rDock is faster than Vina and comparable to Glide. For binding mode prediction, rDock and Vina are superior to Glide. The VS performance of rDock is significantly better than Vina, but inferior to Glide for most systems unless pharmacophore constraints are used; in that case rDock and Glide are of equal performance. The program is released under the Lesser General Public License and is freely available for download, together with the manuals, example files and the complete test sets, at http://rdock.sourceforge.net/
Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
Sergio
S
Ruiz-Carmona
Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
Daniel
D
Alvarez-Garcia
Vernalis (R&D) Ltd, Granta Park, Cambridge, United Kingdom.
Nicolas
N
Foloppe
Amper Programas, Madrid, Spain.
A Beatriz
AB
Garmendia-Doval
Omixon Biocomputing, Budapest, Hungary.
Szilveszter
S
Juhos
Discngine, Paris, France.
Peter
P
Schmidtke
Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
Xavier
X
Barril
Vernalis (R&D) Ltd, Granta Park, Cambridge, United Kingdom; YSBL, University of York, Heslington, York, United Kingdom.
Roderick E
RE
Hubbard
Enspiral Discovery Limited, Cambridge, United Kingdom; Ariana Pharma, Paris, France.
S David
SD
Morley
D055808:Drug Discovery; D008024:Ligands; D009696:Nucleic Acids / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*
D008024:Ligands; D009696:Nucleic Acids; D011506:Proteins