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tooluniverse-protein-structural-annotation-pdb

Given a PDB structure, produce a per-residue annotation table: which residues sit at a binding interface (vs a partner chain), which line a ligand pocket, which are buried (core) vs solvent-exposed (surface), and optionally secondary structure. This is the structural track drawn under a DMS heatmap and the structural prior SAE feature drops are read against. Use when you need to anchor a variant-interpretation or DMS analysis to the protein's actual physical context.

Quality

90%

Does it follow best practices?

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

88%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

Excellent single-file skill content: fully executable tool calls, a genuinely risk-aware workflow with an explicit numbering-validation checkpoint, and domain knowledge Claude would not infer on its own. It is only slightly over-long, with a duplicated intro and some textbook biology in the interpretation table that could be trimmed.

DimensionReasoningScore

Conciseness

The body is dense and skill-specific (numbering offsets, RSA quirks, cutoff conventions) with almost no padding or explanation of things Claude already knows, but a few spots could be tightened — e.g. the interpretation table's 'Common functional role' column restates standard protein biology, and the intro paragraph duplicates the frontmatter description almost verbatim.

4 / 5

Actionability

Every step ships copy-paste-ready calls with full argument signatures ('Structure_annotate_per_residue(pdb_id="6VJJ", target_chain="A", ...)'), the documented return shape, an executable landmark assert, and concrete downstream recipes keyed on exact field names ('by_pos[X]["region"] in ("ligand", "both")').

5 / 5

Workflow Clarity

A clear five-step sequence with an explicit validation checkpoint (Step 3: verify numbering with a UniProt landmark before joining) and an error-recovery path ('If the landmark mismatches, record the offset explicitly ... Do not silently rebase positions'), plus an honest-limitations section covering failure modes.

5 / 5

Progressive Disclosure

No bundle files exist, and the single-file body is well-sectioned with clear headers (inputs, workflow, interpretation table, limitations, cross-references) making it easy to navigate. At ~180 lines, material like the cross-references table and detailed limitations could arguably move to a reference file, so minor organization gains remain.

4 / 5

Total

18

/

20

Passed

Description

88%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A high-quality description: it states concrete, comprehensive capabilities in third person and closes with an explicit 'Use when' clause. Its only weaknesses are a few missing natural trigger synonyms and slight overlap with a downstream consumer skill's DMS/SAE territory.

DimensionReasoningScore

Specificity

The description enumerates multiple concrete outputs — 'which residues sit at a binding interface (vs a partner chain), which line a ligand pocket, which are buried (core) vs solvent-exposed (surface), and optionally secondary structure' — comprehensive and fully concrete coverage of the skill's per-residue annotation capability.

5 / 5

Completeness

It clearly answers 'what' (produce a per-residue annotation table with the enumerated classifications) and 'when' explicitly: 'Use when you need to anchor a variant-interpretation or DMS analysis to the protein's actual physical context.'

5 / 5

Trigger Term Quality

Strong natural terms within the niche ('PDB structure', 'binding interface', 'ligand pocket', 'buried', 'solvent-exposed', 'DMS heatmap', 'variant-interpretation'), but a few common phrasings a user would naturally say are missing (e.g. 'map variants onto the structure', 'surface accessibility', file-style terms like '.pdb').

4 / 5

Distinctiveness Conflict Risk

A clear niche (structural annotation from a PDB for DMS/variant interpretation) with mostly distinct triggers, but the 'DMS heatmap' and 'SAE feature drops' framing overlaps with the referenced downstream consumer skill 'tooluniverse-residue-functional-mechanism-interpretation', creating minor mis-trigger risk.

4 / 5

Total

18

/

20

Passed

Validation

100%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository

mims-harvard/ToolUniverse

Path

plugin/skills/tooluniverse-protein-structural-annotation-pdb/SKILL.md

Reviewed

Table of Contents

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