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Perform high-throughput molecular docking with multiple targets and ligands using AutoDock Vina series engines.

• Molecular docking with multiple target and ligands at the same time.
• Flexible residue declaration for targets.
• Use other Vina-like engines e.g.Qvina2/Qvina-W orSmina.
• Original PDBQT preparation method as distributed with MGLTools.
• Automated PDBQT file preparation.
• Optional ligand energy minimization usingobminimize.
• Output CSV file with all docking results for all modes for an easy access to the docking results.
• Docker support. Run it anywhere!

Dockit can be run withDocker. You must have Docker & docker-compose installed.

git clone https://github.com/aretasg/dockitcd dockit

Installconda first

git clone https://github.com/aretasg/dockitcd dockitconda env create -f environment.ymlconda activate dockit

1. Determine the search box size and centre positioning usingChimera (Tools > Structure/Binding Analysis > Vina) or similar.
2. Define search box and docking parameters for each target indockit_param.csv.
3. Copy protein and ligand PDB files intotargets/PDB andligands/PDB folders, respectively and run:

python app/dockit.py

or if using Docker

docker-compose up

• The calculation will take some time depending on the parameters and the number of files. Results can be found in theresults folder.
• Visualise theresults with a molecular viewer of your choice by loading ligand PDBQT file in theresults folder and target PDB or PDBQT file intargets directory.
• CSV filedockit_results.csv is generated inresults folder with all the docking results.
• Run with-r flag to reset to the pre-run state - PDBQT and result files will be removed.

• Dockit will dock every target against every ligand intargets/PDB andligands/PDB, respectively.
• Dockit is not an input for docking preparation tool. Input files have to be in PDB format. Conversion to PDBQT adds hydrogens and removes non-polar ones.
• Editdockit_param.csv to change any parameters to be run with the docking engine, including search box parameters.
• Run with-m flag perform energy minimization for ligands usingobminimize with default settings.
• Supports declaration of flexible residues for targets. Please look atdockit_param.csv for an example for how to declare flexible residues.
• Supports other Vina-like engines e.g. Qvina2. Please specify the engine name or path to it in theengine column ofdockit_param.csv. Dockit comes installed withvina,qvina2,qvinaw andsmina. You should be able to use any other engine with the same CLI as Vina.
• Specify custom scoring system weights in theweight_* fields ofdockit_param.csv. More about the scoring systemhere.
• Dockit utilises threading to distribute multiple simulations across available cores. Please change thecpu argument to a finite value to ensure distributed processing.
• The necessity of selecting the charges (Kollman/Gasteirger) is obsolete with Vina due to the scoring system being based on hydrophobic and hydrogen bond interactions compared to its predecessor AutoDock 4. Nevertheless, the default charge for targets and ligands are set as Kollman and Gasteirger, respectively.

Written byAretas Gaspariunas. Have a question? You can always ask and I can always ignore.

If you found Dockit useful for your work please acknowledge it by citing this repository.

MIT License.

prepare_* files are distributed as part of MGLTools 1.5.6 and all the ownership is credited to their respective authors (Morris et al., 2009).