free-energy-perturbation

Compute relative and absolute binding free energies with the Open Free Energy toolkit — the rigorous alchemical alternative to docking scores when a congeneric series needs reliable potency ranking. Use this skill to plan a perturbation network over a ligand set, choose atom mappings, run hybrid-topology or separated-topology protocols, and analyse the result — per-edge ΔΔG with uncertainty, cycle-closure error, and mean unsigned error against measured affinities. Also trigger on OpenFE, alchemical transformation, thermodynamic cycle, RBFE, ABFE, SepTop, lambda window, MBAR, cycle closure, or perturbation map.

Version

1.0

License

MIT

Compatibility

Requires Python 3.10+. The bundled scripts plan networks and parse result JSON with the standard library only. Running a calculation needs openfe 1.12+ installed from conda-forge, docker, or singularity — note that `pip install openfe` fetches an unrelated 0.0.12 placeholder. An NVIDIA GPU is effectively mandatory — a single edge is hours of MD.