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Inputs, results, and pipeline code for Modular and Interoperable Workflows for Benchmarking Alchemical Binding Free Energy Calculation Methodologies manuscript.

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RBFE Benchmark

Files and scripts for Modular and Interoperable Workflows for Benchmarking Alchemical Binding Free Energy Calculation Methodologies. For full details, please see the main manuscript, currently available as a preprint at: chemrxiv.

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.

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Inputs, results, and pipeline code for Modular and Interoperable Workflows for Benchmarking Alchemical Binding Free Energy Calculation Methodologies manuscript.

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