TomoDock
About the code
The code automates the process of tomographic docking described in [1]. It takes as input a protein receptor and a set of potential ligands, as well as initial and final geometries of the search spaces for docking and the number of desired scan steps. Then, it computes the search space geometries at each step and attempts to dock each ligand onto the protein using AutoDock Vina [2] as an engine. Thus, the code requires that Vina is installed in the system and accessible to the user.
To download Vina, click here.If you use this code for your research, I kindly ask you to cite Refs. 1 and 2 in your publications.
Download the code
How to use
The code consists of the file tomodock.c. It can be compiled on a standard GNU/Linux distribution with the command
gcc -Wno-unused-result -lm -o tomodock tomodock.c
Important note for Ubuntu users (thanks to Manfred Philipp and Kanika Sharma for informing me of the problem):
due to Ubuntu passing the -as-needed option by default to the linker, users should compile the code with
gcc -Wno-unused-result -o tomodock tomodock.c -lm
In other words, the "-lm" option should be put last on the command line.
Also, consider passing to a proper Linux distribution.
For a comprehensive list of mandatory and optional parameters, including advanced options, just run
./tomodock --help
References
[1] Uzunova, Quareshy, del Genio, and Napier, Open Biology 6, 160139 (2016)
[2] Trott and Olson, J. Comput. Chem 31, 455 (2010)
Release information
Current version
1.8: initial release.
About the code
The code automates the process of tomographic docking described in [1]. It takes as input a protein receptor and a set of potential ligands, as well as initial and final geometries of the search spaces for docking and the number of desired scan steps. Then, it computes the search space geometries at each step and attempts to dock each ligand onto the protein using AutoDock Vina [2] as an engine. Thus, the code requires that Vina is installed in the system and accessible to the user.
To download Vina, click here.If you use this code for your research, I kindly ask you to cite Refs. 1 and 2 in your publications.
Download the code
How to use
The code consists of the file tomodock.c. It can be compiled on a standard GNU/Linux distribution with the command
gcc -Wno-unused-result -lm -o tomodock tomodock.c
Important note for Ubuntu users (thanks to Manfred Philipp and Kanika Sharma for informing me of the problem):
due to Ubuntu passing the -as-needed option by default to the linker, users should compile the code with
gcc -Wno-unused-result -o tomodock tomodock.c -lm
In other words, the "-lm" option should be put last on the command line.
Also, consider passing to a proper Linux distribution.
For a comprehensive list of mandatory and optional parameters, including advanced options, just run
./tomodock --help
References
[1] Uzunova, Quareshy, del Genio, and Napier, Open Biology 6, 160139 (2016)
[2] Trott and Olson, J. Comput. Chem 31, 455 (2010)
Release information
Current version
1.8: initial release.
