jdock is an extended variant of idock which was originally developed by @HongjianLi and is distributed under the same license.
idock is a standalone tool for structure-based virtual screening powered by fast and flexible ligand docking. It was inspired by AutoDock Vina, and is hosted on GitHub at https://GitHub.com/HongjianLi/idock under Apache License 2.0. idock is also available as a web server at istar.
jdock keeps full compatibility with idock and the idock branding remains unchanged across the source code. The only naming change is the name of output binary and GitHub repository.
jdock inherits all features of idock in branch v2.x and tracks changes in that branch. Along with some bug fixes, jdock also adds its own functionalities including but not limited to:
- non-standard residue elimination,
- protonation with pKa values,
- per residue energy summarization and emission,
- alternate location indicator choosing,
- non-compulsory RF-score calculation,
- precision mode to avoid the use of grid maps,
- scoring and docking in a single run,
- compatibility with all kinds of line feedings.
- Linux x86_64 and g++ 8.3.1
- Mac OS X x86_64 and clang 8.0.0
- Windows x86_64 and Visual Studio 2019
jdock depends on the Program Options and Asio components in Boost C++ Libraries. Boost 1.75.0 was tested. There are several ways to get Boost.
# Note: this will download and build from source
vcpkg install boost-program-options boost-asio
nuget install boost_program_options-vc142
sudo apt install libboost-program-options-dev
sudo dnf install boost-program-options boost-devel
jdock is typically statically linked, so the following are also needed and are typically not installed by default
sudo dnf install glibc-static libstdc++-devel libstdc++-static
brew install boost
$Url = "https://sourceforge.net/projects/boost/files/boost-binaries/1.75.0/boost_1_75_0-msvc-14.2-64.exe"
(New-Object System.Net.WebClient).DownloadFile($Url, "$env:TEMP\boost.exe")
Start-Process -Wait -FilePath "$env:TEMP\boost.exe" "/SILENT","/SP-","/SUPPRESSMSGBOXES"
Download Boost 1.75 and unpack the archive to boost_1_75_0/include.
Build on Linux run:
cd boost_1_75_0/include
./bootstrap.sh
./b2 --build-dir=../build/linux_x64 --stagedir=../ -j 8 link=static address-model=64
Or, on Windows run:
cd boost_1_75_0\include
bootstrap.bat
b2 --build-dir=../build/win_x64 --stagedir=../ -j 8 link=static address-model=64
Then add the path of the boost_1_75_0 directory the to the BOOST_ROOT environment variable.
This project uses cross-platform build system CMake to build from source. It detects your environment and decides the most appropriate compiler toolset. The minimum version of CMake required is 3.20. To build, simply run
cmake -B build
cmake --build build --config Release
The generated objects and executable will be placed in the build folder.
Optionally, on Linux or macOS one may install the output binary to the system (usually /usr/local/bin) by running
sudo cmake --install build
On Windows, the script should be run without sudo but under Administrator. The executable will be copied to an individual directory under Program Files.
Visual Studio 2019 solution and project files are provided. To compile, simply run
msbuild /t:Build /p:Configuration=Release
Or one may open idock.sln in Visual Studio 2019 and do a full rebuild.
The generated objects will be placed in the obj folder, and the generated executable will be placed in the ..\bin folder.
First add jdock to the PATH environment variable.
To display a full list of available options, simply run the program without arguments
jdock
The examples folder contains several use cases. For example, to dock the ligand TMC278 against HIV-1 RT of PDB ID 2ZD1,
jdock -r receptors/2ZD1.pdbqt -l ligands/T27 -x 49.712 -y -28.923 -z 36.824 --size_x 18 --size_y 18 --size_z 20
Or one can instruct jdock to load the options from a configuration file
cd examples/2ZD1/T27
jdock --config idock.conf
- Switched build system from Make to cross-platform CMake
- Added GitHub Actions workflows for building and releasing binaries
- Merged changes from upstream HongjianLi/idock/v2.x for adding support for ten rare chemical elements
- Added --ignore_errors program option
- Initial public release based on idock v2.2.3
- Added computation of residue energy contribution
- Added support for protonation via pka
- Added per residue output for gauss1/gauss2/gauss/repulsion/steric/hydrophobic/hbonding/nonsteric/total scoring combinations
- Added program option shortcuts
- No RF score computation by default (use --rf_score to revert)
- Removed precompiled binaries in conformance with the US export control regulation
- More changes see the Feature section above
Maozi Chen, Zhiwei Feng, Siyi Wang, Weiwei Lin, Xiang-Qun Xie. MCCS, a scoring function-based characterization method for protein-ligand binding. Briefings in Bioinformatics. 2020, October 14. DOI: 10.1093/bib/bbaa239 PubMed: 33051641
Hongjian Li, Kwong-Sak Leung, and Man-Hon Wong. idock: A Multithreaded Virtual Screening Tool for Flexible Ligand Docking. 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), pp.77-84, San Diego, United States, 9-12 May 2012. DOI: 10.1109/CIBCB.2012.6217214