rDock: a Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

rDock is a fast and versatile open-source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for high-throughput virtual screening (HTVS) campaigns and binding mode prediction studies.

rDock is mainly written in C++ and accessory scripts and programs are written in C++, Perl or Python languages.

The full rDock software package requires less than 50 MB of hard disk space and it is compilable (at this moment, only) in all Linux computers.

Thanks to its design and implementation [rDock2014], it can be installed on a computation cluster and deployed on an unlimited number of CPUs, allowing HTVS campaigns to be carried out in a matter of days.

Besides its main Docking program, the rDock software package also provides a set of tools and scripts to facilitate preparation of the input files and post-processing and analysis of results.

About

Features

_images/dock1.jpg

Fig. 1 The above image illustrates the first binding mode solution for ASTEX system 1hwi, with an RMSD of 0.88 Å.

Docking preparation

Define cavities using known binders or with user-supplied 3D coordinates. Allow -OH and -NH2 receptor side chains to rotate. Add explicit solvent molecules and structural waters. Supply pharmacophoric restraints as a bias to guide docking.

Pre-processing of input files

Define common ligand structure for performing tethered docking (requires Open Babel Python bindings). Sort, filter or split ligand files for facilitating parallelization. Find HTVS protocol for optimizing calculation time. Pre-calculate grids to decrease subsequent calculation times.

Post-processing and analysis of results

Summarize results in a tabular format. Sort, filter, merge or split results files. Calculate RMSD with a reference structure taking into account internal symmetries (requires Open Babel Python bindings).

Binding mode prediction

Predict how a ligand will bind to a given molecule. The ASTEX non-redundant test set for proteins and DOCK and rDock test sets for RNA have been used for validating and comparing rDock with other programs.

HTVS

Run for million of compounds in short time by exploiting the capabilities of computer calculation farms. Ease of parallelization in relatively unlimited CPUs to optimize HTVS running times. The DUD set has been used for validating rDock and comparing its performance to other reference docking programs.

_images/dock2.jpg

Fig. 2 In red mesh, definition of the cavity obtained by execution of rbcavity program.

History

The rDock program was developed from 1998 to 2006 by the software team at RiboTargets (subsequently Vernalis (R&D) Ltd) [RiboDock2004]. In 2006, the software was licensed to the University of York for maintenance and distribution.

In 2012, Vernalis and the University of York agreed to release the program as open-source software [rDock2014]. This version is developed with support from the University of Barcelona –- http://sourceforge.net/projects/rdock/.

Contributor concordat

rDock adheres both to No Code of Conduct and Code of Merit.

References

If you are using rDock in your research, please cite:

rDock2014(1,2)

Ruiz-Carmona, S., Alvarez-Garcia, D., Foloppe, N., Garmendia-Doval, A. B., Juhos S., et al. (2014) rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids. PLoS Comput Biol 10(4): e1003571. doi:10.1371/journal.pcbi.1003571

Former software reference provided for completeness:

RiboDock2004

Morley, S. D. and Afshar, M. (2004) Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®. J Comput Aided Mol Des, 18: 189–208. doi:10.1023/B:JCAM.0000035199.48747.1e

Download

Please visit rDock sourceforge page for most up to date releases.

Getting started

In this section, you have the documentation with installation and validation instructions for first-time users.

You can read the documentation in HTML format in this same page, or you can download it in PDF format following this link.

To continue with a short validation experiment (contained in the Getting started guide), please visit the Validation experiments section.

Support

If you are having some trouble regarding usage, compilation, development or anything else, you can use different options to ask for support.

Mailing lists

If you are having any kind of trouble, you have any questions or anything related to general usage of the program please search and use our mailing lists.

Issue tracker

Mostly for developers and code-related problems. If you find any bug, e.g., please go to tickets section in rDock sourceforge website.

Indices and tables