DockFlow
DockFlow aims at making docking campaigns and virtual screening easy tasks accessible by everyone.
Its main advantage is to properly organize results and manage errors to make the user's experience as productive as possible.
It is also completely integrated in the ChemFlow environment, making it super efficient to rescore docking poses with other scoring functions, run MD simulations, or automatically produce tables and graphs for a thorough analysis.
This version of DockFlow implements PLANTS to run the docking experiments. For this reason, it is only able to read mol2 files.
DockFlow requires 4 things from the user :
- A directory that will contain all the files and folders mentioned below : the run folder.
- A directory containing the receptor in a mol2 file.
- A directory containing the ligands in mol2 files.
ℹ️ Each mol2 file can contain one or several ligands. The number of ligands in each file should be distributed equally for maximum performance when running in parallel. - A configuration file : DockFlow.config.
ℹ️ The configuration file should either be generated by running ConfigFlow, which guides you through a graphical interface, or copied from the$CHEMFLOW_HOME/config_filesdirectory.
- Mandatory parameters
Start by stating the absolute path to your receptor file and ligand directory.
For the definition of the binding site, PLANTS uses a sphere so you will need to provide x, y and z coordinates of the center of the sphere as well as its radius.
Since DockFlow's search algorithm and scoring function perform quite fast, we recommend asking for at least 25 docking poses per ligand.
- Optionnal parameters
You can add other parameters for PLANTS, such as docking with a structural water molecule.
Finally, and most importantly, you can choose how to run the experiment :
- local : run on the current computer in serial,
- parallel : run locally using GNU parallel for a more efficient use of your computer resources,
- mazinger : run on a compute cluster equipped with PBS.
