LightDock is a protein-protein, protein-peptide and protein-DNA docking framework based on the Glowworm 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 and it has support for the use of pre-calculated conformers for both receptor and ligand.
LightDock protocol and the updates to make use of residue restraints have been published in Oxford Bioinformatics journal. Please cite these references if you use LightDock in your research:
LightDock: a new multi-scale approach to protein–protein docking
Brian Jiménez-García, Jorge Roel-Touris, Miguel Romero-Durana, Miquel Vidal, Daniel Jiménez-González and Juan Fernández-Recio
Bioinformatics, Volume 34, Issue 1, 1 January 2018, Pages 49–55, https://doi.org/10.1093/bioinformatics/btx555
LightDock has the following dependencies:
- NumPy (http://www.numpy.org/)
- Scipy (http://www.scipy.org/)
- Cython (http://cython.org/)
- BioPython (http://biopython.org)
- ProDy (http://prody.csb.pitt.edu/)
- Freesasa (http://freesasa.github.io/)
Optional dependencies are:
- MPI4py (if you plan to use MPI support which is experimental at the moment, http://pythonhosted.org/mpi4py/)
3.1.1. Installing NumPy, Scipy, Cython, Biopython and ProDy
pip3 install numpy, scipy, cython, biopython, pyparsing, prody
|WARNING: Issues installing ProDy in macOS have been reported. In case you are not able to install ProDy using
3.2. Install LightDock
The fastest way to install LightDock is to use
pip3 install lightdock
3.3. Alternative installations
Please visit the repository documentation on GitHub for alternative installation.
The complete documentation about how to run the LightDock protocol can be found at https://lightdock.org.
5. Get Help
LightDock is being actively developed and some issues may arise or you may get some extra help to run LightDock. In those cases, there are two main ways to get help:
- Read the FAQ in case your problem is known
- Open a new issue in this repository
- Or write an email to firstname.lastname@example.org
LightDock is available under GPLv3 License. See LICENSE document for more details.