.. _dock-documentation: |Dock|: a fast, versatile, and open-source program for docking ligands to proteins and nucleic acids ==================================================================================================== |Dock| 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. |Dock| is mainly written in C++ and accessory scripts and programs are written in C++, Perl or Python languages. The full |Dock| 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 |Dock| 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: About ----- .. _download: Download ^^^^^^^^ Please visit RxDock GitLab page for most up to date releases. * `Download a released version `__ * `Get the latest code using git `__ Features ^^^^^^^^ .. figure:: _images/dock1.jpg 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 |Dock| test sets for RNA have been used for validating and comparing |Dock| with other programs. High-throughput virtual screening 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 |Dock| and comparing its performance to other reference docking programs. .. figure:: _images/dock2.jpg In red mesh, definition of the cavity obtained by execution of ``rbcavity`` program. History ^^^^^^^ The RiboDock 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 under the name rDock. 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 `__ -- `sourceforge.net/projects/rdock `__. The development of rDock stalled in 2014. Since 2019, `RxTx `__ is developing a fork of rDock under the name RxDock. License ^^^^^^^ |Dock| is licensed under GNU LGPL version 3.0. .. toctree:: :maxdepth: 2 license Contributor concordat ^^^^^^^^^^^^^^^^^^^^^ |Dock| adheres both to No Code of Conduct and Code of Merit. .. toctree:: :maxdepth: 2 code-of-counduct code-of-merit References ^^^^^^^^^^ If you are using |Dock| in your research, please cite [rDock2014]_. Former software reference provided for completeness is [RiboDock2004]_. .. [rDock2014] 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 `__ .. [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 `__ .. _getting-started-guide: Getting started guide --------------------- In this section, you have the documentation with installation and validation instructions for first-time users. To continue with a short validation experiment (contained in the :ref:`Getting started guide `), please visit the :ref:`Validation experiments section `. .. toctree:: :maxdepth: 2 :caption: Contents: getting-started-guide/overview getting-started-guide/quick-and-dirty-installation getting-started-guide/prerequisites getting-started-guide/unpacking getting-started-guide/building getting-started-guide/validation-experiments .. _reference-guide: Reference guide --------------- In this section you can find the documentation containing full explanation of all |Dock| software package and features. For installation details and first-users instructions, please visit :ref:`Installation ` and :ref:`Getting started ` sections. .. toctree:: :maxdepth: 2 :caption: Contents: reference-guide/preface reference-guide/acknowledgements reference-guide/introduction reference-guide/configuration reference-guide/cavity-mapping reference-guide/scoring-functions reference-guide/docking-protocol reference-guide/system-definition-file reference-guide/atom-typing reference-guide/file-formats reference-guide/programs reference-guide/appendix .. _user-guide: User guide ---------- .. toctree:: :maxdepth: 2 :caption: Contents: user-guide/docking-in-3-steps user-guide/docking-strategies user-guide/multi-step-protocol-for-htvs user-guide/calculating-roc-curves user-guide/running-docking-jobs-in-parallel user-guide/pharmacophoric-restraints .. _developer-guide: Developer guide --------------- .. toctree:: :maxdepth: 2 :caption: Contents: developer-guide/target-platforms developer-guide/build-system developer-guide/coding-standards developer-guide/documentation developer-guide/versioning .. _support: 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 the discussion section of `RxDock channel on Telegram `__. Issue tracker ^^^^^^^^^^^^^ Mostly for developers and code-related problems. If you find a bug, please report it in `issues section in RxDock GitLab project `__.