OpenBPMD - evaluating ligand pose stability using metadynamics

Background

OpenBPMD is an open source implementation of binding pose metadynamics (BPMD). Based on work by Clark et al, 2016. Primarily built for reranking docked poses out of a list of candidates generated by a docking program. OpenBPMD biases ligands using metadynamics and evaluates how stable they are during the simulation. Recommended to be used in conjunction with grand to optimise water networks around the ligand before subjecting it to metadynamics.

Installation & Usage

The dependencies needed for running the scripts can be installed with conda:

conda create -n openbpmd
conda activate openbpmd

conda install -c conda-forge -c omnia openmm
conda install -c conda-forge mdanalysis
conda install -c conda-forge mdtraj
conda install -c conda-forge parmed

Once the dependencies have been installed, running OpenBPMD involves simply running one of the Python scripts. Have a look at the examples/ directory for further instructions on how to run and analyse the OpenBPMD results.

References

1. A. J. Clark, P. Tiwary, K. Borrelli, S. Feng, E. Miller, R. Abel, R. A. Friesner, B. J. Berne, J. Chem. Theory Comput. 2016, 12, 6, 2990–2998, DOI:https://doi.org/10.1021/acs.jctc.6b00201
2. D. Lukauskis, M. L. Samways, S. Aureli, B. P. Cossins, R. D. Taylor, F. L. Gervasio, J. Chem. Inf. Model. 2022, 62, 23, 6209–6216, DOI:https://doi.org/10.1021/acs.jctc.6b00201