Commit f8cf3922 authored by Vedran Miletić's avatar Vedran Miletić

Add README file in markdown format

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# 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, 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
![The above image illustrates the first binding mode solution for ASTEX
system 1hwi, with an RMSD of 0.88 Å.](docs/_images/dock1.jpg)
#### 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
#### 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
#### 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.
![In red mesh, definition of the cavity obtained by execution of
`rbcavity` program.](docs/_images/dock2.jpg)
### History
The rDock program was developed from 1998 to 2006 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 developed with support from the University of Barcelona --
### License
rDock is licensed under [GNU LGPL version 3.0](
### References
If you are using rDock in your research, please cite:
* 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.
Former software reference provided for completeness:
* 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.
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