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Virtual screening with
Autodock |
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Virtual screening with
Autodock |
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| Licensing/Downloading Information |
Library screening documentation |
Download distribution |
| Dockres documentation |
LIBRARY SCREENING: A collection of utilities are in the subdirectory "fullscreen" of the distribution directory. The most important one, fullscreen.csh takes as input a directory name containing the ligands in Tripos' .mol2 format and a macromolecule file in Autodock's .pdbqs or .pdbqt format and runs Autodock on a user-specifed number of CPU's. There is a detailed documentation for fullscreen.csh, as well as all the other utilities assisting in setting up the screening as well as post-processing.
NOTE, that several of the scripts in this collection require customization to specify the location of various directories.
POST-PROCESSING: The mainstay of post-processing is the program Dockres. It reads the log file created by Autodock (version 3.0.5 and version 4) and extracts the top scoring poses. Dockres does not require that the screening is done with fullscreen.csh - it runs on any set of log files.
The extraction can be subject to various filters. e.g., the residue nearest to the ligand, the closest approach to a preselected macromolecule atom or ligand charge.
The program also calculates distributions of various properties of the ligand set (e.g., molecular weight, number of hydrogen bond donors) and the distribution of docking sites as well as the distribution of docking free energies per target residue.
Also, selected poses can be extracted into PDB files that contains the macromolecule as well.