Package: lightdock
1. SynopsisLightDockis a protein-protein, protein-peptide and protein-DNA docking framework based on theGlowworm Swarm Optimization(GSO) algorithm.The LightDock framework is highly versatile, with many options that can be further developed and optimized by the users: it can accept any user-defined scoring function, can use local gradient-free minimization, the simulation can be restrained from the beginning to focus on user-assigned interacting regions,it supports residue restraints in both receptor and ligand partners.2. ReferenceLightDock protocol and the updates to make use of residue restraints have been published inOxford Bioinformaticsjournal. Please cite these references if you use LightDock in your research:LightDock: a new multi-scale approach to protein–protein dockingBrian Jiménez-García, Jorge Roel-Touris, Miguel Romero-Durana, Miquel Vidal, Daniel Jiménez-González and Juan Fernández-RecioBioinformatics, Volume 34, Issue 1, 1 January 2018, Pages 49–55,https://doi.org/10.1093/bioinformatics/btx555LightDock goes information-drivenJorge Roel-Touris, Alexandre M.J.J. Bonvin,Brian Jiménez-GarcíaBioinformatics, btz642; doi:https://doi.org/10.1093/bioinformatics/btz642Integrative Modeling of Membrane-associated Protein AssembliesJorge Roel-Touris,Brian Jiménez-García& Alexandre M.J.J. BonvinNat Commun11, 6210 (2020); doi:https://doi.org/10.1038/s41467-020-20076-53. InstallationLightdock software is compatible and it has been tested with the followings OS:macOS: El Capitan, Sierra, High Sierra, Mojave, Catalina.GNU/Linux: Ubuntu 16+, Debian Stretch+, Scientific Linux 6+, CentOS 6+.100% compatible withGoogle Colab platformMicrosoft Windows is not officially supported, despite many parts of the protocol might be able to run. Please use it at your own risk. If you wish to contribute testing and developing LightDock for Windows, please contact us.3.1. DependenciesLightDock has the following dependencies:NumPy (http://www.numpy.org/)Scipy (http://www.scipy.org/)Cython (http://cython.org/)ProDy (http://prody.csb.pitt.edu/)Freesasa (http://freesasa.github.io/)Optional dependencies are:MPI4py (if you plan to use MPI support,http://pythonhosted.org/mpi4py/)3.2. Install LightDockThe fastest way to install LightDock is to usepip:pipinstalllightdock4. DevelopmentFor development and extension of the LightDock code, please follow these instructions:4.1. CloneClone this repository:gitclonehttps://github.com/lightdock/lightdock.git4.2. Compile Python C and Cython extensionsPlease make sure dependencies are already installed (via pip, package manager, etc.):numpy>=1.17.1scipy>=1.3.1cython>=0.29.13prody>=1.10.11freesasa>=2.0.3It is recommended to create a virtual environment and install it:virtualenvvenvsourcevenv/bin/activatecdlightdock
pipinstall-e.If not using pip or setuptools for development, there is as bash script to compile all the extensions:cdlightdock
./setup.sh4.3. Add Lightdock to your pathAdd the following lines to your~/.bashrcfile, don't forget to change/path/to/lightdock:# LightDockexportLIGHTDOCK_HOME="/path/to/lightdock"exportPATH=$PATH:$LIGHTDOCK_HOME/binexportPYTHONPATH=$PYTHONPATH:$LIGHTDOCK_HOMEDon't forget to apply the changes:source~/.bashrc4.4. TestingYou can run LightDock tests:cdlightdock
nosetests5. DocumentationThe complete documentation about how to run the LightDock protocol and several tutorials and use cases can be found athttps://lightdock.org/tutorials.6. Get HelpLightDock is being actively developed and some issues may arise or you may need extra help to run LightDock. In those cases, there are two main ways to get help:Read theFAQin case your problem was already reportedOpen anew issue in this repositoryOr write an email tolightdocking@gmail.com(we will do our best to answer your questions as soon as possible)7. LICENSELightDock is available under GPLv3 License. SeeLICENSEdocument for more details.