Automated Pipeline for Consensus Scoring Between Docking Programs

This pipeline facilitates the running of consensus scoring between docking programs. The maximum number of programs supported is five.

Inputs

1. SDF format file from the docking program. Place this into a directory named after the docking program (one word) within the working directory.
2. All utilities that come with this package.

Usage

Example for consensus of poses scoring (RMSD of 2 Angstroms) for five docking programs:

snakemake --cores 1 --snakefile Snakefile autodock_glide_fred_icm_vina_docking_consensus_plot.png --config number='five'

Where Autodock, Glide, Fred, Icm, and Vina are docking programs.

Another example for three docking programs:

snakemake --cores 1 --snakefile Snakefile autodock_glide_fred_docking_consensus_plot.png --config number='three'

Note: Adjust the '--config number' as per your requirement.

Dependencies

You will need several dependencies to execute this code. The most crucial are:

• Openbabel 2.4.1 and its pybel wrapper

conda install -c conda-forge/label/cf202003 openbabel=2.4.1

Preliminary Setup

1. Ensure you have SnakeMake installed in your conda environment (activate it before installing). Installation instructions for SnakeMake can be found here.

Note: Replace 'base' with your conda environment name during the installation process.

2. Modify the config.yaml file to contain the score field name in the sdf file with the docked poses and scores.

Configuration Variables

Some customizable variables include:

• Consensus Type: Determines the type of consensus (e.g., two-way, three-way, etc.) especially when using five docking programs. Perhaps you only want a consensus between a minimum number of programs.

  • Adjust by setting the -cons flag in the Snakefile to your desired number (maximum is 5).

• Consensus RMSD: Defines the agreement between two poses from the corresponding docking programs.

  • Adjust by setting the -rmsd flag in the Snakefile to your preferred float value.

By default, the values are set to a three-way consensus and a 2.0 Angstrom RMSD pose agreement.