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AC esmfold2

Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al. 2026, github.com/Biohub/esm). Single-sequence and MSA modes; protein, DNA, RNA, ligand (CCD/SMILES), modified residues. FoldBench Ab-Ag 50-55%, PPI 70-77% DockQ-pass. Also covers the ESMC-{300M,600M,6B} protein language models from the same release: masked-LM logits, hidden states, mutation scoring, contact prediction, and the SAE interpretability head. MIT-licensed weights on HuggingFace org `biohub`. Use this skill when: (1) Predicting complex structures with single-sequence input, (2) Validating designed binders with ESMFold2-Fast, (3) Running ESMFold2 with MSA input, (4) Getting ESMC embeddings or per-residue mutation scores, (5) Choosing kernel backend and sampling-step settings for paper-faithful throughput.

aipoch/open-science Agent Skills author: aipoch Apache-2.0 3 files body ≈ 2 394 tokens Open the sourcegithub.com↗ analyzed 2 d ago

Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al.

As a process C 52/100 · Has gaps — weak spots: result and completion, inputs and preconditions, running it twice

AnalyzerGitHubSoftware developmentAI and agentstype and topics are labelled automatically from the skill text
Runs in: Claude / Claude Code ChatGPT / Codex Gemini CLI Cursor GitHub Copilot / VS Code Qwen Code Kimi Code CLI Z.ai (GLM) DeepSeek (Deep Code) Mistral Vibe LangChain (deepagents) OpenClaw Goose OpenCode
JSON
Technical rating
A
95/100
safety, quality, tests
Safety 60%
99
Quality 40%
88
Run on models
none yet
Process rating
C
52/100
Has gaps
Result and completion w 14
0
Inputs and preconditions w 11
0
Progress reporting w 2
0
the three weakest of ten parameters · all ten

How to improve

    For the model run — optional
    • Your own cases (evals/evals.json, 4–6 real requests with expected answers): the full check would then run those instead of a model-drafted suite.
    • A spec.yaml with trigger phrases and assertions — a behaviour contract for CI; `skilltest init` writes a template.

    Guard findings · 1

    ✓ No critical or high findings

    Medium and low: 1
    • low Secrets in code secret-high-entropy-token SKILL.md:122
      High-entropy token-like string (may be an id, hash or a credential) (documentation table row)
      | `ESMF…ase{300M,600M,6B}-step{250k..1500k}` | —                         | —           | —   | 15 critic ensemble     |
      table

    Files scanned: 3. Evidence is masked. Grey chips explain why severity was lowered.

    Against the Agent Skills spec

    • note frontmatter-key unknown frontmatter key "requirements"

    Process rating: all ten parameters 52/100

    • 0Result and completion. Does not say what the result is
    • 0Inputs and preconditions. Does not say what the process needs to start
    • 0Progress reporting. Says nothing while it works
    • 30Running it twice. 2 mutating operations with no state check
    • 50When it triggers. No condition that starts the skill
    • 50Failures and branches. 0 branches, has a failure section
    • 60Tools and files. Uses tools (python) that frontmatter does not declare
    • 100Steps. 6 steps
    • 100Consistency. Name and required fields are in place
    • 100Execution cost. Instruction body is 2394 tokens
    • low 10 top-level sections: this looks like several domains in one skill

    Everything here is measured from the skill text rather than judged by a model, so the numbers are checkable. A parameter weighs more when it is a more common reason for the process to stall.

    Quality signals

    • +5Description has no quoted example phrases that should trigger the skill
    • +4Description does not say when NOT to use the skill (false activations)
    • +3Output format is not stated: the model decides each time
    • +2Single-language instructions
    • +3Description length 791: enough signal without eating the budget
    • +4Structure: 11 headings
    • +3Step-by-step instructions: 6 items
    • +4Has examples (5 code blocks)
    • +4Reference files are cited in the instructions (2 of 2)
    • +1License stated

    Quality base 70; lint remarks subtract, signals add up to 100. Result: 88.