Skip to content
Protein docking framework based on the GSO algorithm
Branch: master
Clone or download
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
bin
docs Added docs in PDF format May 22, 2019
examples Added documentation for restraints, new full 4G6M example Jan 10, 2019
lightdock Fixed test after function name changed May 23, 2019
.gitignore
CODE_OF_CONDUCT.md Code of conduct Nov 29, 2017
CONTRIBUTING.md Created Contributing.md file Nov 29, 2017
ISSUE_TEMPLATE.md Simplified ISSUE_TEMPLATE.md Apr 16, 2019
LICENSE Version 0.4.0 May 25, 2017
README.md Small FAQ Apr 16, 2019
_config.yml Set theme jekyll-theme-cayman Jun 2, 2018
run_tests.sh Version 0.4.0 May 25, 2017

README.md

LightDock

Table of Contents

1. Introduction

LightDock is a protein-protein, protein-peptide and protein-DNA docking framework based on the Glowworm Swarm Optimization (GSO) algorithm.

The framework is written in the Python programming language (version 2.7) and allows the users to incorporate their own scoring function.

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.

2. Reference

The first version of the LightDock protocol was published in Oxford Bioinformatics journal. Please cite this reference 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

A preprint about the implementation details and performance of the new protocol for including residue restraints is avaiable at biorxiv:

LightDock goes information-driven
Jorge Roel-Touris, Alexandre M.J.J. Bonvin, Brian Jiménez-García
bioRxiv 595983; doi: https://doi.org/10.1101/595983

3. Installation

3.1. Dependencies

LightDock has the following dependencies:

3.1.1. Installing NumPy, Scipy, Cython, Biopython, Nose and MPI4py

NumPy, Scipy, Cython, Biopython, Nose and MPI4py libraries are usually available as packages in most of GNU/Linux distributions. For example, to install them in Ubuntu execute:

sudo apt-get update && apt-get install python-numpy python-scipy cython python-biopython python-nose python-nose2 python-mpi4py

Make sure all libraries are from the Python 2.7.x series.

3.1.2. Installing ProDy

To install ProDy library, the simplest way is to use pip (you can use sudo to install it system-wide):

pip install -U ProDy

You may also need to install pyparsing dependency:

pip install pyparsing

More instructions on how to install it can be found in the official documentation (http://prody.csb.pitt.edu/downloads/).

3.1.3. Installing FreeSASA (optional)

In case of using cpydock scoring function or to execute the tests, Freesasa library has to be installed and compiled with the python-binding options. Tested version in LightDock is 1.1 (https://github.com/mittinatten/freesasa/tree/1.1). To install freesasa 1.1, please follow these instructions (change path/to/install):

git clone https://github.com/mittinatten/freesasa.git
cd freesasa
git checkout tags/1.1
autoreconf -i
./configure --enable-python-bindings --prefix=path/to/install
make
make install

For more recent versions of freesasa, please check the instructions for installing it on its Github (https://github.com/mittinatten/freesasa).

3.2. Download LightDock

The fastest way to install LightDock is to use git to clone the repository from GitHub:

git clone https://github.com/brianjimenez/lightdock.git

A directory called lightdock is now available. This is the path necessary for setting the enviroment variable LIGHTDOCK_HOME in your bash. Change your ~/.bashrc accordingly (add the following lines to your ~/.bashrc):

export LIGHTDOCK_HOME=/path/to/lightdock/folder
export PATH=$PATH:$LIGHTDOCK_HOME/bin:$LIGHTDOCK_HOME/bin/post:$LIGHTDOCK_HOME/bin/support
export PYTHONPATH=$PYTHONPATH:$LIGHTDOCK_HOME

3.3. Compilation of high-intensive calculation source code

Once the library dependencies are installed, a compilation of some high-intensive calculation parts is required. To do so, a script is provided:

cd ${LIGHTDOCK_HOME}/bin/setup
./setup.sh

3.4. Testing the framework (optional)

LightDock makes use of nosetests library for testing the different parts of the framework. There are two levels of testing: unitary and regression.

Library unit tests. To run them execute:

cd $LIGHTDOCK_HOME
./run_tests.sh lib

Regression short tests. To run them execute:

cd $LIGHTDOCK_HOME
./run_tests.sh reg

Regression long tests. To run them execute (this may take several minutes):

cd $LIGHTDOCK_HOME
export LIGHTDOCK_LONG_TEST=true
./run_tests.sh reg

NOTE: some tests may fail depending on float accuracy in your installation. This is probably not relevant unless you plan to run lightdock using that piece of code. Please, open an issue in this GitHub repository to get help.

4. Documentation

This GitHub README.md file is intended as an installation guide.

The complete documentation about how to run the LightDock protocol can be found at:

https://brianjimenez.github.io/lightdock/

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:

  1. Read the FAQ in case your problem is known
  2. Open a new issue in this repository
  3. Or write an email to b.jimenezgarcia@uu.nl
You can’t perform that action at this time.