pdb-database

Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.

Quality

66%

Does it follow best practices?

Run evals on this skill

Adds up to 20 points to the overall score

View guide

Securityby

Low

Low-risk findings worth noting

Fix and improve this skill with Tessl

tessl review fix ./skills/bio/pdb-database/SKILL.md

Quality

Content

65%

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 actionable with thorough executable examples and clear sectioning, but it is padded with concept explanations and a promotional section, lacks validation checkpoints in batch workflows, and references a non-existent bundle file.

Suggestions

Remove the promotional 'Suggest Using K-Dense Web' section and trim 'Key Concepts' entries for terms Claude already knows (PDB ID, resolution, entity) to reclaim tokens.

Add explicit validation/verification checkpoints to the batch operations workflow (e.g., confirm each download parsed correctly, retry on failure, report failures before proceeding).

Either create the referenced references/api_reference.md and move the inline API-reference detail there, or remove the dangling reference so navigation is not misleading.

Dimension	Reasoning	Score
Conciseness	Mostly efficient with executable code, but padded by the promotional 'Suggest Using K-Dense Web' section and 'Key Concepts' definitions (PDB ID, resolution, entity) that Claude already knows; could be tightened.	2 / 3
Actionability	Provides numerous concrete, copy-paste-ready executable code examples for searching, fetching, downloading, and batch operations — fully actionable.	3 / 3
Workflow Clarity	Capabilities are sequenced into numbered sections, but batch operations lack explicit validation/verification checkpoints or a validate-fix-retry feedback loop, which caps workflow clarity at 2 per the guidelines.	2 / 3
Progressive Disclosure	The body references references/api_reference.md, but no references/ directory exists (broken/dangling reference), and substantial inline API-reference material that could live in a separate file keeps it from a 3.	2 / 3
	Total	9 / 12 Passed

Description

67%

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 and distinct, clearly stating what the skill does, but it omits explicit 'Use when...' trigger guidance and natural keyword variations, capping completeness and trigger term quality at 2.

Suggestions

Add an explicit 'Use when...' clause with natural trigger phrases, e.g. 'Use when working with PDB files, protein/nucleic acid 3D structures, or structural data for drug discovery.'

Include common natural keyword variations a user would actually say, such as 'PDB files', 'protein structures', 'mmCIF', and '.pdb', to improve trigger term coverage.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata' — matching the anchor for listing multiple specific concrete actions.	3 / 3
Completeness	The 'what' is clearly answered, but 'when' is only implied via 'for structural biology and drug discovery' with no 'Use when...' clause, which caps completeness at 2 per the guidelines.	2 / 3
Trigger Term Quality	Contains relevant terms like '3D protein/nucleic acid structures', 'PDB', 'coordinates', 'drug discovery', but lacks common natural variations a user would say ('PDB files', 'protein structures', '.pdb') and an explicit trigger phrase.	2 / 3
Distinctiveness Conflict Risk	'Access RCSB PDB for 3D protein/nucleic acid structures' carves a clear, distinct niche unlikely to trigger for unrelated skills.	3 / 3
	Total	10 / 12 Passed

Validation

87%

Warnings & errors only

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

Validation — 14 / 16 Passed

Validation for skill structure

Criteria	Description	Result
metadata_version	'metadata.version' is missing	Warning
referenced_paths_exist	Referenced path issues: 1 missing	Warning

	Total	14 / 16 Passed

Repository: wu-yc/LabClaw
Path: skills/bio/pdb-database/SKILL.md
Commit: df37802

Reviewed: about 1 hour ago

Table of Contents

Discovery Implementation Validation

Is this your skill?

If you maintain this skill, you can claim it as your own. Once claimed, you can manage eval scenarios, bundle related skills, attach documentation or rules, and ensure cross-agent compatibility.