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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 folder with a set of PDB files for each host system and SDF files for each set of ligands for each system.
  • util.py a set of utility methods and base classes used throughout this repository.
  • examples a directory with notebooks for example calculations and analyses

Relative binding free energies

The following systems are obtained from the OpenFF Protein-Ligand Benchmarks:

  • TYK2
  • PTP1B