bio-free-energy-calculations skillA
bio-free-energy-calculations is agent-read markdown (skill) from pku-yuangroup/openai4s: Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda scheduling, soft-core potentials, MBAR/BAR analysis, cycle-closure validation, and protocol-appropriate enhanced sampling. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, .
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
## Version Compatibility Reference examples tested with: OpenFE 1.7+, OpenMM 8.1+, GROMACS 2024+, AMBER pmemd 22+, alchemlyb 2.1+, pymbar 4.0+, RDKit 2024.09+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `openfe --version`; `gmx --version`; `pmemd.cuda --version` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Free Energy Calculations Predict binding free-energy differences (RBFE) or standard binding free energies (ABFE) using alchemical methods. FEP+ is a commercial workflow and OpenFE is an open-source framework. Accuracy and cost vary substantially with system, perturbation, force field, setup, sampling, and evaluation design; report the protocol and benchmark relevant to the intended decision. The Boltz-2 report includes benchmark-specific comparisons with FEP methods but does not replace prospective validation on the project chemistry. …
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How to install
mdr add pku-yuangroup/openai4s/bio-free-energy-calculations@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-free-energy-calculations@sha256:3c56d4b2ce53cb7bPin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_auaxfhejrfgpy2o2)
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_auaxfhejrfgpy2o2 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-free-energy-calculations GET https://markdownregistry.com/api/v1/blob/3c56d4b2ce53cb7b7c81af83182d1474b96e1920f600770d60e04cde741823cd
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