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pdb-database

Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D similarity) or automated structural data ingestion for structural biology and drug discovery workflows.

68

Quality

84%

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Passed

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SKILL.md
Quality
Evals
Security

Quality

Content

76%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.

The body is actionable and well-structured with an executable example and a genuine reference file, but the batch workflow lacks explicit validation/feedback loops and minor conciseness and organization gaps remain.

Suggestions

Add an explicit validate→fix→retry feedback loop to the batch processing section (e.g., verify each download parses before proceeding, retry on failure) to lift workflow clarity above the batch cap.

Tighten the example script (drop verbose print formatting or move ancillary parsing into a short snippet) to reduce token overhead.

Move the more detailed Implementation Details (schema vs GraphQL, format comparisons) into references/api_reference.md, leaving the SKILL.md body a leaner overview pointing to it.

DimensionReasoningScore

Conciseness

The body is largely efficient with executable code and domain-specific API notes Claude would not trivially know, though the ~70-line example script and a few explanatory prose lines (e.g., format comparisons) could be trimmed slightly.

4 / 5

Actionability

It provides a fully executable end-to-end script, concrete download endpoints, and a copy-paste GraphQL pattern covering the common search/fetch/download/parse cases.

5 / 5

Workflow Clarity

The example script has a clear numbered sequence with minimal checks (raise_for_status, no-results guard), but the batch processing section — a batch operation — lacks explicit validate→fix→retry checkpoints, capping the score per the batch-operation guideline.

3 / 5

Progressive Disclosure

Structure is good with well-signaled sections and a real one-level-deep reference (references/api_reference.md, verified to exist) for advanced detail, though some Implementation Details are inlined and only a single reference file is offered.

4 / 5

Total

16

/

20

Passed

Description

92%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 strong description that clearly states capabilities and triggers in third person, with comprehensive concrete actions and a well-defined niche. The only gap is slight synonym/extension coverage in the trigger terms.

DimensionReasoningScore

Specificity

The description lists multiple concrete actions — 'search, download, and programmatically retrieve 3D macromolecular structures and metadata' plus 'structure discovery (text/sequence/3D similarity)' — giving comprehensive coverage rather than just naming the domain.

5 / 5

Completeness

It explicitly answers 'what' ('Access the RCSB PDB to search, download, and programmatically retrieve...') and 'when' ('use when you need structure discovery... or automated structural data ingestion'), with concrete trigger phrases for both.

5 / 5

Trigger Term Quality

Strong natural keywords are present ('PDB', 'protein', '3D structures', 'structural biology', 'drug discovery', 'sequence similarity'), but it omits common synonyms and file extensions (e.g., '.pdb', 'protein structures' as a phrase), leaving a few natural terms missing.

4 / 5

Distinctiveness Conflict Risk

The RCSB PDB / structural biology niche is highly specific with distinct triggers, making conflict with other skills minimal.

5 / 5

Total

19

/

20

Passed

Validation

93%

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

Validation15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

15

/

16

Passed

Repository
aipoch/medical-research-skills
Reviewed

Table of Contents

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