Files and scripts for Modular and Interoperable Workflows for Benchmarking Alchemical Binding Free Energy Calculation Methodologies. For full details, please see the main manuscript (previously: preprint).
analysis - contains the ipynb used to generate the analysis and figures for the main manuscript.
inputs - contains the parameterised proteins and the ligand structure files, generated networks, predicted network performance, and experimental values.
results - contains the csv files of the edge and ligand results for each system.
pipeline - contains the code and scripts used for setting up, running, and analysing the simulations.
Below is an outline of the pipeline:
In order to run the RBFE bechmark, please follow instructions in the pipeline folder.