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pocket-detection

Multi-method binding pocket detection and druggability assessment. Grid-based, fpocket, and P2Rank detection with druggability scoring, visualization, and cross-structure comparison.

65

Quality

82%

Does it follow best practices?

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SecuritybySnyk

Medium

Suggest reviewing before use

SKILL.md
Quality
Evals
Security

Quality

Content

85%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.

A highly actionable, well-sequenced body: executable commands throughout, explicit validation checkpoints before, during, and after runs, and strong error-recovery guidance. The main structural weakness is progressive disclosure — the bundled references/methods_guide.md is never linked from the body, and its method-detail content is partially duplicated inline instead of being delegated to it.

Suggestions

Link references/methods_guide.md from the body (e.g. under Method Comparison: "For algorithm details, tuning parameters, and when to use each method, see [methods_guide.md](references/methods_guide.md)) so the bundled reference is discoverable.

Delegate detailed method strengths/limitations and tuning guidance to the guide and keep only a brief pointer in SKILL.md to reduce duplication.

Trim the redundancy between the Overview, Key capabilities, and When to Use sections, which restate the same capability list three times.

DimensionReasoningScore

Conciseness

The body is command-first with almost no padding for concepts Claude already knows; tables (script reference, druggability classes, method comparison) are dense and useful. Minor over-explanation exists — the Overview, Key capabilities, and When to Use sections restate the same capabilities three times — keeping it below the lean anchor. Not a 3 because the excess is minor trimming, not genuinely unnecessary explanation.

4 / 5

Actionability

Every workflow is a complete, copy-paste-ready command with real flags and file names, the full pipeline (Workflow 6) includes the exact JSON-parsing shell glue for handing off pocket centers to docking, and output JSON schemas are shown verbatim. This matches the fully-executable anchor covering common cases.

5 / 5

Workflow Clarity

Sequences are clear with explicit validation checkpoints: Quick Verification commands validate the install before running, the Species Validation section validates input before proceeding, the method-agreement rule (centers within 5 A) validates results, and Troubleshooting provides ordered fix-and-retry feedback loops ("adjust the script's parameters... Do NOT abandon the skill scripts"). Not a 4 because checkpoints are present at every stage, not just most.

5 / 5

Progressive Disclosure

Scored against the actual bundle: the four scripts are clearly and accurately referenced via the Script Reference table and inline commands, but references/methods_guide.md exists in the bundle and is never referenced from the body, making it undiscoverable. Additionally, the body inlines method-strengths and tuning guidance that overlaps the guide's content, which is the should-be-separate-inline pattern. Not a 4 because an entire reference file being orphaned is more than a minor organization gap.

3 / 5

Total

17

/

20

Passed

Description

75%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, specific description in third person that clearly states what the skill does, with distinctive trigger terms (fpocket, P2Rank, druggability). Its one significant weakness is the absence of an explicit "Use when..." clause, which both caps completeness and leaves natural trigger synonyms ("active site", "binding site") uncovered.

Suggestions

Append an explicit trigger clause, e.g. "Use when the user asks to find binding pockets or active sites, assess druggability, or compare binding sites across structures."

Add natural synonyms users would say — "active site", "binding site", "where does the ligand bind" — to broaden trigger coverage.

Optionally add a boundary hint (e.g. "for docking into detected pockets, use molecular-docking") to further reduce conflict risk with adjacent skills.

DimensionReasoningScore

Specificity

The description lists multiple specific concrete actions — "Grid-based, fpocket, and P2Rank detection", "druggability scoring", "visualization", "cross-structure comparison" — in third person, with comprehensive coverage of the skill's capabilities. It matches the anchor for multiple specific concrete actions with comprehensive coverage; there is no missing capability area.

5 / 5

Completeness

The "what" is clearly and concretely answered (detection, scoring, visualization, comparison), but there is no "Use when..." clause or equivalent explicit trigger guidance, which caps completeness at 3 per the judging guidelines. Not a 2 because the "what" half is fully explicit rather than vague.

3 / 5

Trigger Term Quality

Good natural keyword coverage: "binding pocket detection", "druggability assessment", plus distinctive tool names (fpocket, P2Rank). However, common user phrasings like "active site", "binding site", or "find binding pockets" are absent, so it falls just short of the comprehensive-synonyms anchor. Not a 3 because the included terms are natural phrases users would actually say, not jargon.

4 / 5

Distinctiveness Conflict Risk

It carves out a clear niche (pocket detection/druggability) with distinct triggers including the unique method names fpocket and P2Rank, minimizing conflict risk with adjacent skills like docking or binding-affinity prediction. It does not fit the minor-overlap anchor for 4 because the method names and druggability framing are uniquely attributable to this skill.

5 / 5

Total

17

/

20

Passed

Validation

87%

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

CriteriaDescriptionResult

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/chemistry/pocket-detection/SKILL.md

Reviewed

Table of Contents

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