Open Free Energy Benchmark Systems

A set of benchmark systems to validate the OpenFE components.

Contents

The openfe_benchmark repository contains:

• A file for each system in the benchmark set (e.g. tyk2.py). These hold methods for creating the free energy network and the system components necessary to calculate the benchmark.
• A data directory with a set of PDB files for each host system and SDF files for each set of ligands for each system.
• A scripts directory with examples of how to set up calculations such as:

• bfe: binding free energy
• hfe: hydration free energy
• sfe: solvation free energy (requires external tools)

• examples a directory with notebooks for example calculations and analyses

Available Systems

The available systems are indexed in the benchmark_system_indexing.yml file. This file provides a comprehensive list of the benchmark systems along with tags representing whether they can be used for bfe or sfe calculations and whether there are cofactors in the system. These systems can also be explored in Python, as demonstrated in the notebook 1_initializing_benchmark_data.ipynb.

Additional Resources

• OpenFE Documentation: https://docs.openfree.energy
• GUFE Documentation: https://gufe.openfree.energy
• Example Notebooks: See examples/ directory for:
  • 1_initializing_benchmark_data.ipynb - How to use the benchmark systems API
  • 2_benchmark_data_with_openfe.ipynb - Using a BenchmarkData system with OpenFE tools
  • building_networks.ipynb - Creating ligand networks