idock is a multithreaded virtual screening tool for flexible ligand docking for computational drug discovery. It is inspired by AutoDock Vina, and is hosted by GitHub at https://GitHub.com/HongjianLi/idock under Apache License 2.0.
- idock invents its own thread pool in order to reuse threads and maintain a high CPU utilization throughout the entire screening procedure. The thread pool parallelizes the precalculation of scoring function, the creation of grid maps, and the execution of Monte Carlo tasks.
- idock estimates the capacity of every vector structure and intensively utilizes right-value reference, a new feature in the C++11 standard, to avoid frequent memory reallocation.
- idock flattens Vina's tree-like recursive data structure of ligand into simple linear array structure to ensure a high data cache hit rate and easy coding.
- idock accelerates the assignment of atom types by making use of residue information for receptor and branch information for ligand.
- idock supports as many as 29 chemical elements including rare ones like Zn, Fe, Mg, Ca, Mn, Cu, Na, K, Hg, Ni, Co, Cd, As and Sr.
- idock supports reading and writing compressed ligand files with gzip and bzip2.
- idock enables automatic recovery and restarts docking from the previous stopping point.
- idock reports progress every 10% Monte Carlo tasks per ligand in a neat manner.
- idock outputs putative inter-molecular hydrogen bonds for each predicted conformation.
- idock outputs per-atom free energy for protein-ligand interaction hotspot detection.
- idock outputs summary for each predicted conformation into a CSV file for subsequent analysis.
- idock provides precompiled executables for 32-bit and 64-bit Linux, Windows, Mac OS X, FreeBSD and Solaris.
- idock can be used as a backend docking engine for igrow, a multithreaded ligand growing tool for structure-based molecule design.
- idock is now available as a service at istar.
- Ubuntu 11.10 x86_64 and GCC 4.6.1
- Ubuntu 11.10 x86_64 and CLANG 3.0
- Ubuntu 11.10 x86_64 and Intel C++ Compiler 12.1.2
- Fedora 16 x86_64 and GCC 4.6.2
- Fedora 16 x86_64 and Intel C++ Compiler 12.1.2
- Arch Linux 3.5.2 x86_64 and GCC 4.7.1
- Arch Linux 3.4.2 x86_64 and CLANG 3.1
- Arch Linux 3.4.2 x86_64 and Intel C++ Compiler 12.1.2
- CentOS 6.3 x86_64 and GCC 4.4.6
- FreeBSD 9.0 x86_64 and CLANG 3.1
- Solaris 11 11/11 and GCC 4.5.2
- Mac OS X 10.7.4 x86_64 and CLANG 3.1
- Windows 7 SP1 x64 and Windows SDK 7.1
- Windows 7 SP1 x64 and Visual Studio 2010 SP1
- Windows 7 SP1 x64 and Intel C++ Compiler 12.1.2
- Windows 8 x64 and Visual Studio 2012 Ultimate
idock depends on Boost C++ Libraries. Boost 1.46.0, 1.46.1, 1.47.0, 1.48.0, 1.49.0, 1.50.0, 1.51.0 and 1.52.0 are tested. The Boost libraries required by idock are Chrono, System, Thread, Filesystem, Program Options and Iostreams.
The Makefile uses GCC as the default compiler. To compile, simply run
make
CLANG is also supported.
make TOOLSET=clang
Intel C++ Compiler is also supported.
make TOOLSET=intel
One may modify the Makefile to use a different compiler or different compilation options.
The generated objects will be placed in the obj folder, and the generated executable will be placed in the bin folder.
Visual Studio 2012 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 2012 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 idock to your PATH environment variable.
To display a full list of available options, simply run the program without arguments
idock
The examples folder contains several use cases. For example, to dock the ligand TMC278 against HIV-1 RT of PDB ID 2ZD1,
cd examples/2ZD1/T27
One can supply the options from command line arguments
idock --receptor ../../../receptors/2ZD1.pdbqt --ligand_folder ../../../ligands/T27 --output_folder output --center_x 49.712 --center_y -28.923 --center_z 36.824 --size_x 18 --size_y 18 --size_z 20
Or one can instruct idock to load the options from a configuration file
idock --config idock.cfg
For comparison against AutoDock Vina
vina --config vina.cfg
Documentations in both HTML and LaTeX formats can be esaily created by running doxygen
doxygen doxygen
The created documents will be placed in doc folder. To compile LaTeX files into PDF, one must have pdflatex installed.
cd doc/latex
make
The generated PDF will be refman.pdf.
- Output ligand efficiency.
- Updated Visual Studio 2012 project settings.
- Fixed a bug of repeatly executing the same Monte Carlo tasks.
- Updated the logo.
- Added a new example 2VQZ.
- Output putative inter-molecular hydrogen bonds for each predicted conformation.
- Precompiled idock for Windows using Visual Studio 2012.
- Upgraded Visual Studio project from 2010 to 2012.
- Fixed a bug of aligning columns in log.csv.
- Fixed a bug of writing repeated energies to log.csv when compiling idock with clang 3.1 on Mac OS X and FreeBSD.
- Supported CentOS 6.3.
- Upgraded boost from 1.50.0 to 1.51.0.
- Added a new example 2ZNL.
- Supported a new chemical element strontium (Sr).
- Updated clang from 3.0 to 3.1.
- Supported file error detection in output folder.
- Supported reading and writing ligands in gzip and/or bzip2 format.
- Output the number of hydrogen bonds for each conformation.
- Fixed a segmentation fault bug when the number of heavy atoms exceeds 100.
- Added two new examples 2IQH and 1HCL.
- Reverted to file stem only in the ligand column in log.csv to shrink size.
- Added sufficient commas in log.csv to align rows.
- Skipped already docked ligands.
- Prevented dead loop by limiting the number of initial conformation trials.
- Used a more compact and constant data structure for ligand representation.
- Refactored program option
conformationstomax_conformations. - Output full path to docked ligands to csv.
- Removed boost::math::quaternion and implemented a lightweight quaternion class.
- Added BibTeX citation to the idock paper accepted and to be published in CIBCB 2012.
- Added bash scripts for running AutoDock Vina for docking ZINC clean drug-like ligands.
- Output predicted total free energy, predicted inter-ligand free energy and predicted intra-ligand free energy to docked PDBQT files.
- Output predicted free energy for each heavy atom to docked PDBQT files.
- Updated Boost from 1.48.0 to 1.49.0.
- Supported compilation on Windows 8 Consumer Preview x64 with Visual Studio 11 Ultimate Beta.
- Added a new example with PDB code 1V9U.
- Supported compilation on Solaris 11 11/11 with GCC 4.5.2.
- Added program option
csvfor dumping docking summary sorted in the ascending of predicted free energy. - Profiled by the Valgrind tool suite to ensure zero memory leak.
- Replaced a switch statement by table lookup to decrease indirect branch misprediction rate.
- Added move constructors for several classes to boost performance.
- Revised the precision of coordinates and free energy to be 3 digits.
- Parallelized the precalculation of scoring function.
- Fixed a numerical bug when docking a ligand of only one single heavy atom.
- Added support for Mac OS X 10.7.2 and FreeBSD 9.0.
- Added support for docking ligands created by igrow.
- Changed the version control system from TFS to Git.
- Project migrated from CodePlex to GitHub.
- Tested Solaris 11, clang 3.0, and Intel C++ Compiler v11.
- Provided Visual C++ solution, project and bat files to ease recompilation on Windows.
- Added precompiled executables for both 32-bit and 64-bit Linux and Windows.
- Added program option
configto allow users to specify a configuration file. - Added thread-safe progress bar.
- Output predicted free energy of the top 5 conformations.
- Reverted the evaluation of intra-molecular free energy to Vina's implementation to obtain better RMSD for certain cases.
- Initial release at CodePlex.
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
