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tooluniverse-protein-structure-retrieval

Protein structure retrieval from RCSB PDB, PDBe, and AlphaFold with disambiguation, quality assessment (resolution, R-factor, pLDDT), and metadata. Distinguishes high-quality experimental (X-ray under 2 Angstrom) vs predicted vs medium-quality structures. Use for fetching protein structures, structure-quality comparison, and selecting structures for drug design or modeling.

76

Quality

93%

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

87%

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

The content is highly concise and immediately actionable, with concrete tool calls and decision tables that a model can execute directly. Its only gap is the absence of an explicit retrieve-and-verify feedback loop in the workflow, which keeps workflow_clarity at 2 for an otherwise strong skill.

Suggestions

Add a lightweight verification checkpoint in Phase 2 (e.g., confirm metadata/quality fields are non-empty and cross-check PDB ID resolution before composing the report), turning it into a retrieve→verify→report feedback loop.

Make the Phase 2 example code parameterized rather than hardcoding pdb_id = "4INS" so the snippet reads as a reusable template instead of a single illustrative call.

DimensionReasoningScore

Conciseness

The body is lean, assumes Claude's domain competence, and avoids explaining basic structural-biology concepts; tables and code blocks are tight with every line carrying information.

3 / 3

Actionability

Provides concrete, copy-paste-ready tool calls (tu.tools.<fn>(...)) with parameters, a worked PDB example, fallback chains, and explicit quality-tier thresholds a model can apply directly.

3 / 3

Workflow Clarity

The four-phase sequence is clear and explicitly gated (Phase 0 ask/skip criteria, retrieve-silently instruction), but no explicit verification/feedback loop checks that retrieved data is internally consistent before reporting; reporting-only workflows are low-risk, so it caps at 2 rather than dropping.

2 / 3

Progressive Disclosure

Single self-contained SKILL.md (~130 lines) with well-organized sections and no external references; under the simple-skills rule, well-organized one-file structure earns 3.

3 / 3

Total

11

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12

Passed

Description

100%

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

The description is specific, third-person, and explicitly states both capabilities and use-trigger contexts, with concrete quality-tier language. It is slightly long but every clause earns its place. This is a strong, well-differentiated description.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — retrieval, disambiguation, quality assessment, metadata, and quality-tier discrimination — each tied to concrete metrics (resolution, R-factor, pLDDT).

3 / 3

Completeness

Explicitly answers both what it does (retrieval with disambiguation/quality/metadata) and when to use it via the closing 'Use for fetching protein structures, structure-quality comparison, and selecting structures for drug design or modeling.' clause.

3 / 3

Trigger Term Quality

Includes natural user-facing terms like 'fetching protein structures', 'structure-quality comparison', and 'selecting structures for drug design or modeling' that map to how a user would phrase the need.

3 / 3

Distinctiveness Conflict Risk

Occupies a clear niche (protein-structure retrieval across named sources) with distinct triggers tied to structural biology and drug design, making overlap with unrelated skills unlikely.

3 / 3

Total

12

/

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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