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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.

72

Quality

87%

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

85%

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

A well-structured, highly actionable skill body with a strong validation checkpoint and honest operational limitations. The weakest dimension is conciseness, as the one-tool workflow runs long and repeats some description content.

Suggestions

Trim the "When to use this skill" section, which largely restates the frontmatter description; keep only the DMS/SAE-specific triggers and the "Not for" boundary.

Condense the Step 1 prose and the Honest Limitations items into tighter bullets so the single atomic-tool call stays the focal point of the body.

DimensionReasoningScore

Conciseness

The body is information-dense and avoids explaining basics Claude knows, but at ~170 lines wrapping a single atomic tool it is on the verbose side: the "When to use" section partly reiterates the description and several step prose blocks could be tightened.

2 / 3

Actionability

Concrete, copy-paste-ready Python with real values — Structure_annotate_per_residue(pdb_id="6VJJ", ...), the assert landmark check, and the by_pos lookup — fully executable rather than pseudocode.

3 / 3

Workflow Clarity

Five clearly sequenced steps with an explicit validation checkpoint (Step 3 verify-numbering assert plus offset-recovery guidance and "Do not silently rebase positions"), providing a real feedback loop for a fragile join operation.

3 / 3

Progressive Disclosure

No bundle files are provided and none are needed; the single self-contained file is well organized with clear section headers and a one-level cross-reference table, so the simple-skill allowance applies.

3 / 3

Total

11

/

12

Passed

Description

90%

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 strong, specific description with explicit what-and-when guidance and a clear niche. The only ding is the second-person "you" in the trigger, which the rubric penalizes on specificity.

DimensionReasoningScore

Specificity

Lists multiple concrete actions ("produce a per-residue annotation table", "which residues sit at a binding interface", "which line a ligand pocket", "buried (core) vs solvent-exposed"), which meets the 3 anchor, but the trigger clause uses second person ("Use when you need to anchor"), so the rubric's voice guideline reduces specificity by 1.

2 / 3

Completeness

It explicitly answers both what ("produce a per-residue annotation table" with the listed classifications) and when ("Use when you need to anchor a variant-interpretation or DMS analysis"), matching the explicit-trigger anchor.

3 / 3

Trigger Term Quality

The "Use when" clause and body include natural domain terms a user would say — "variant-interpretation", "DMS analysis", "PDB structure", "binding interface", "ligand pocket" — giving good coverage rather than abstract jargon.

3 / 3

Distinctiveness Conflict Risk

The niche is sharp — a per-residue structural annotation track drawn under a DMS heatmap — and the role-relative-to-partner-chain framing makes it unlikely to trigger for the wrong skill.

3 / 3

Total

11

/

12

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.

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
mims-harvard/ToolUniverse
Reviewed

Table of Contents

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