bio-free-energy-calculations
bio-free-energy-calculations is a Chemistry & materials skill for AI agents, published by GPTomics in the bioSkills repository on GitHub. Skillspace rates bio-free-energy-calculations C (79/100) and it passed the safety scan; the rating is based on static analysis only.
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, or validating SAR predictions.
- Grade
- C
- Quality
- 79 / 100
- Safety
- Passed
- GitHub stars
- 1,025
Unproven: rated by static analysis only, not yet compared head-to-head.
This rating describes the version of the repository we crawled; it may have changed since, so go by its current files.
Our review
- Architecture
- 97 / 100
- Maturity
- Structured: ships references or scripts
- Security scan
- No issues found
- License
- MIT
- Adoption
- Adopted by 0 other repositories, in 1 collections
- Scope
- Vendor-specific: built around one product. Uses public packages OpenFE, GROMACS, AMBER, OpenMM, alchemlyb
Not checked yet
- Not judged on the rubric yet (not a contender in its category)
- No blind task eval yet
- Sibling files (scripts, references) not fetched; security scan covers SKILL.md only
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