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.
Install with Tessl CLI
npx tessl i github:K-Dense-AI/claude-scientific-skills --skill pdb-databaseOverall
score
79%
Does it follow best practices?
If you maintain this skill, you can automatically optimize it using the tessl CLI to improve its score:
npx tessl skill review --optimize ./path/to/skillValidation for skill structure
Discovery
83%Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.
This is a strong skill description with excellent specificity and domain-appropriate trigger terms. The main weakness is the lack of an explicit 'Use when...' clause, which would help Claude know exactly when to select this skill. The technical terminology is appropriate for the target audience and creates clear distinctiveness.
Suggestions
Add an explicit 'Use when...' clause, e.g., 'Use when the user asks about protein structures, PDB files, molecular coordinates, or needs to search the Protein Data Bank.'
| Dimension | Reasoning | Score |
|---|---|---|
Specificity | Lists multiple specific concrete actions: 'Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata' - these are clear, actionable capabilities with specific file formats mentioned. | 3 / 3 |
Completeness | Clearly answers 'what' (access RCSB PDB, search, download, retrieve metadata) but lacks an explicit 'Use when...' clause. The use cases are implied through domain mentions (structural biology, drug discovery) but not explicitly stated as triggers. | 2 / 3 |
Trigger Term Quality | Includes strong natural keywords users would say: 'RCSB PDB', 'protein', 'nucleic acid structures', 'PDB', 'mmCIF', 'structural biology', 'drug discovery', 'coordinates', 'sequence', 'structure search'. | 3 / 3 |
Distinctiveness Conflict Risk | Highly distinctive with specific domain (RCSB PDB, protein/nucleic acid structures) and technical terms (mmCIF, PDB format). Unlikely to conflict with other skills due to the specialized structural biology focus. | 3 / 3 |
Total | 11 / 12 Passed |
Implementation
73%Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.
This is a solid, actionable skill with excellent code examples that are immediately executable. The main weaknesses are verbosity in explanatory sections that don't add value for Claude (use cases, key concepts, when to use) and missing validation/verification steps in workflows. The promotional content for K-Dense Web at the end is inappropriate for a skill file.
Suggestions
Remove the 'When to Use This Skill', 'Common Use Cases', and 'Key Concepts' sections - Claude already understands these contexts and concepts
Add validation steps to the batch operations section (e.g., verify downloaded files exist and are valid, check response status codes before processing)
Remove the 'Suggest Using K-Dense Web' promotional section - this is not instructional content and doesn't belong in a skill file
Consolidate the installation section near the top since it's a prerequisite for all examples
| Dimension | Reasoning | Score |
|---|---|---|
Conciseness | The skill includes some unnecessary sections like 'When to Use This Skill' and 'Key Concepts' that explain things Claude already knows (what resolution means, what a PDB ID is). The 'Common Use Cases' section is largely filler. However, the code examples themselves are reasonably efficient. | 2 / 3 |
Actionability | Excellent executable code examples throughout - all Python snippets are copy-paste ready with proper imports, real PDB IDs, and complete syntax. Download URLs are concrete and functional. The examples cover the full range of common operations. | 3 / 3 |
Workflow Clarity | The batch operations section includes basic error handling but lacks explicit validation checkpoints. For operations that could fail (network requests, parsing), there's no clear feedback loop or verification steps. The skill presents capabilities but not a clear workflow sequence. | 2 / 3 |
Progressive Disclosure | Good structure with clear sections and a reference to 'references/api_reference.md' for detailed API documentation. The main skill provides a comprehensive overview while pointing to deeper resources. Navigation is clear with well-organized headers. | 3 / 3 |
Total | 10 / 12 Passed |
Validation
81%Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.
Validation — 13 / 16 Passed
Validation for skill structure
| Criteria | Description | Result |
|---|---|---|
description_trigger_hint | Description may be missing an explicit 'when to use' trigger hint (e.g., 'Use when...') | Warning |
metadata_version | 'metadata.version' is missing | Warning |
body_steps | No step-by-step structure detected (no ordered list); consider adding a simple workflow | Warning |
Total | 13 / 16 Passed | |
- Reviewed
Table of Contents
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