Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add PKU-YuanGroup/OpenAI4S --skill bio-chemoinformatics-free-energy-calculationsgit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-chemoinformatics-free-energy-calculations)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-chemoinformatics-free-energy-calculations"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-chemoinformatics-free-energy-calculations/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-chemoinformatics-free-energy-calculations"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-chemoinformatics-free-energy-calculations.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00117 | $0.04375 |
| Opus 5 | $0.00059 | $0.02188 |
| Sonnet 5 | $0.00023 | $0.00875 |
| Haiku 4.5 | $0.00012 | $0.00438 |
Grade A, and why
bio-free-energy-calculations scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
This is a copy
95% identical to bio-free-energy-calculations — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 310 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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>thenhelp(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.
For docking input poses, see chemoinformatics/virtual-screening. For pose validation before FEP, see chemoinformatics/pose-validation. For ML alternatives, see chemoinformatics/ml-docking-rescoring.
FEP Method Taxonomy
| Method | Cost / pair | Accuracy | Use case | Fails when |
|---|---|---|---|---|
| FEP+ (Schrödinger) | System- and protocol-dependent GPU cost | Published commercial RBFE workflow | Commercial lead optimization | License and reproducibility constraints |
| OpenFE RBFE | System- and protocol-dependent GPU cost | Open-source RBFE with documented protocols | Open-source campaigns | Mapping/setup/sampling require review |
| OpenFE ABFE | Generally more setup and sampling than one RBFE edge | Standard binding free energy | No congeneric reference ligand required | Restraints and end-state corrections |
| GROMACS / AMBER RBFE | Implementation-dependent | Custom alchemical workflows | Expert-controlled setup | Manual validation burden |
| FEP-SPell-ABFE | Protocol/system-dependent | Automated ABFE workflow | Evaluate published and project benchmarks | Limited adoption |
| QligFEP v2.1 | Protocol/system-dependent | Q-based ligand FEP | Evaluate published and project benchmarks | Different approximations/tooling |
| MM/PBSA / MM/GBSA | Lower-cost endpoint analysis | Approximate endpoint score | Exploratory within-series comparison | Entropy, sampling, and model dependence |
| Boltz-2 affinity | seconds GPU | 0.66 Pearson on reported FEP benchmark subset | ML alternative; reported >=1000x lower cost | Novel chemotypes |
| ALEPB / EE-AMBER | Protocol/system-dependent | Specialized methods | Evaluate matched evidence | Limited tooling |
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 12d ago First seen · 310 lines · 117 tokens per session scan A 3c56d4b2ce53
bio-free-energy-calculations is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 117 tokens to every session and 4,375 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it A with 0 findings. It is 95% identical to bio-free-energy-calculations, differing in 12 lines, and is treated as a copy.
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