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=7.4.2
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.
Citing OpenBPMD
The manuscript that validates OpenBPMD by replicating the results of Clark et al, 2016 is currently in review.