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

73%

Does it follow best practices?

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Securityby

Low

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tessl review fix ./backend/cli/skills/databases/pdb-database/SKILL.md

Quality

Content

65%Weight 40%Scale 1-3

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

Highly actionable with strong executable examples, but the body is verbose and monolithic, with some explanatory padding and missing validation checkpoints for batch operations. Splitting deeper detail into references and trimming basics would improve it.

Suggestions

Add explicit validation/verification steps (e.g. verify a downloaded file parses, or confirm batch fetch counts match the input list) and a retry loop for failed entries.

Trim the Key Concepts and Overview sections of fundamentals Claude already knows; keep only PDB-specific nuances.

Move the more exhaustive search/GraphQL examples into references/api_reference.md so SKILL.md stays a lean overview pointing to detail.

Dimension	Reasoning	Score
Conciseness	Mostly efficient with concrete code, but the Overview and Key Concepts sections explain basics Claude largely knows (e.g. PDB ID, Resolution, Entity) and could be tightened.	2 / 3
Actionability	Provides numerous fully executable, copy-paste-ready code blocks covering search, fetch, GraphQL, download, parsing, and batch operations with specific endpoints and identifiers.	3 / 3
Workflow Clarity	Capabilities are clearly sequenced into numbered sections and batch ops use try/except, but there are no explicit validation/verification checkpoints for batch or download operations, capping this at 2.	2 / 3
Progressive Disclosure	A real references/api_reference.md is clearly signaled one level deep, but the ~300-line body expands all five capabilities fully inline, resembling reference material that could be split out further.	2 / 3
	Total	9 / 12 Passed

Description

82%Weight 40%Scale 1-3

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 specific, distinctive description with good trigger-term coverage, weakened only by the absence of an explicit 'Use when…' trigger clause. Adding one would lift completeness to full marks.

Suggestions

Append an explicit trigger clause, e.g. 'Use when searching for or downloading protein/nucleic acid 3D structures, retrieving PDB metadata, or working with structural biology / drug-discovery datasets.'

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata' — matching the anchor for several specific concrete actions.	3 / 3
Completeness	It clearly answers 'what' but only implies 'when' via 'for structural biology and drug discovery' rather than an explicit 'Use when…' clause, which per the guidelines caps completeness at 2.	2 / 3
Trigger Term Quality	Covers natural terms users would say — '3D protein/nucleic acid structures', 'PDB/mmCIF', 'structural biology', 'drug discovery' — giving good coverage rather than jargon-only phrasing.	3 / 3
Distinctiveness Conflict Risk	The RCSB PDB / 3D macromolecular structure niche is clearly distinct and unlikely to trigger for the wrong skill.	3 / 3
	Total	11 / 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
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	14 / 16 Passed

Repository: synthetic-sciences/openscience
Path: backend/cli/skills/databases/pdb-database/SKILL.md
Commit: dc00e07

Reviewed: 11 days ago

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