Overview

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

The rDock program was developed from 1998 to 2006 (formerly known as RiboDock [RiboDock2004]) by the software team at RiboTargets (subsequently Vernalis (R&D) Ltd.). 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. This version is licensed under GNU LPGL version 3.0 with support from the University of Barcelona – rdock.sourceforge.net.

The major components of the platform now include fast intermolecular scoring functions (van der Waals, polar, desolvation) validated against protein and RNA targets, a Genetic Algorithm-based stochastic search engine, a wide variety of external structure-based drug discovery (SBDD) derived restraint terms (tethered template, pharmacophore, noe distance restraints), and novel Genetic Programming-based post-docking filtering. A variety of scripts are provided to perform automated validation experiments and to launch virtual screening campaigns.

This introductory guide is aimed at new users of rDock. It describes the minimal set of steps required to build rDock from the source code distribution, and to run one of the automated validation experiments provided in the test suite distribution. The instructions assume that you are comfortable with simple Linux command line administration tasks, and with building Linux application from makefiles. Once you are familiar with these steps you should proceed to the User and Reference Guide for more detailed documentation on the usage of rDock.