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tooluniverse-small-molecule-discovery

Small molecule identification, characterization, and procurement — PubChem, ChEMBL, BindingDB, ADMET-AI, SwissADME, eMolecules, Enamine. Covers compound name to structure to activity to ADMET properties to commercial sourcing. Use for chemical biology, lead identification, probe selection, and the full small-molecule discovery pipeline.

60

Quality

71%

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SecuritybySnyk

Low

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tessl review fix ./plugin/skills/tooluniverse-small-molecule-discovery/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

63%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 well-structured, highly actionable tool-usage skill with concrete invocations, worked examples, fallback chains, and honest limitation notes. Its weaknesses are redundancy (duplicate tool tables, repeated caveats, restated textbook drug-likeness rules) and the absence of any progressive disclosure — a 350-line monolith whose API reference belongs in a separate file.

Suggestions

Merge the 'Key Tools' and 'Tool Parameter Reference' tables into one table (or move the merged table to references/tool_reference.md) — they list ~25 of the same tools with overlapping parameter columns, and the BindingDB-unavailable caveat is repeated in four sections.

Trim or move the 'Key drug-likeness rules' block and the Lipinski caveats in 'Domain Reasoning' — Claude already knows Lipinski/Veber cutoffs; keep only the skill-specific guidance ('match the profile to the target and route').

Replace placeholder arguments like CANONICAL_SMILES in Phases 2-6 with a single concrete worked example (as Phase 1 does for imatinib) so every phase is copy-paste ready, and add a quick validity check after identity resolution (e.g., confirm a CID was returned before running ADMET tools).

DimensionReasoningScore

Conciseness

The body is dense and tool-focused, but there is measurable waste: the 'Key Tools' table (lines 49-79) and the 'Tool Parameter Reference' table (lines 247-274) duplicate ~25 tools with overlapping parameter columns; BindingDB's flakiness is repeated in at least four places (KEY PRINCIPLES, Phase 3, Fallback Chains, Limitations); and the 'Key drug-likeness rules' block (Lipinski/Veber/lead-like cutoffs) plus the Domain Reasoning paragraph restate standard chemistry knowledge Claude already has. This fits the score-3 anchor (mostly efficient but includes some unnecessary explanation or could be tightened); it is not the score-2 'noticeably verbose, several padded sections' case since most sections carry non-obvious operational facts (list-vs-string SMILES, URL-only returns).

3 / 5

Actionability

Guidance is highly concrete: exact tool names with parameters (e.g., 'ChEMBL_search_activities(molecule_chembl_id="CHEMBL941", pchembl_value__gte=6, limit=50)'), a fully worked Phase 1 example with real values (imatinib -> CID 5291 -> CHEMBL941), a pChEMBL interpretation table, and a fallback-chain table. It falls short of score 5 because later phases use placeholders ('CANONICAL_SMILES', 'SCAFFOLD_SMILES') rather than copy-paste-ready literals, leaving minor gaps; it is well above score 3 since these are real tool invocations, not pseudocode.

4 / 5

Workflow Clarity

Six clearly sequenced phases with an explicit 'ID resolution priority' ordering, per-phase expected outputs ('-> Returns: ...'), and a Fallback Chains table that functions as error-recovery guidance (BindingDB -> ChEMBL, ADMET-AI -> SwissADME, Enamine API 500 -> URL). This matches the score-4 anchor (clear sequence, most checkpoints present, minor validation gaps); it does not reach score 5 because there are no explicit validation steps confirming lookups succeeded before proceeding (e.g., verifying a CID resolved before running ADMET), and the workflows are read-only so the destructive/batch cap does not apply.

4 / 5

Progressive Disclosure

The skill is a single 350-line SKILL.md with no bundle files (references/, scripts/, assets/ do not exist), and roughly 90 lines are API-reference tables ('Key Tools', 'Tool Parameter Reference') that the score-2/3 anchors treat as content that belongs in a separate reference file. Section headers and horizontal rules give it real structure, so it sits at the score-3 anchor (some structure, content that should be separate is inline) rather than score 2, and short of score 4 since there is no split at all despite the file being long.

3 / 5

Total

14

/

20

Passed

Description

78%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 names a concrete pipeline, specific tools, and an explicit 'Use for...' clause in third person. Its main gaps are missing natural trigger synonyms (SMILES, analog, availability) and a use-case-domain framing of 'when' rather than user-facing trigger phrases.

DimensionReasoningScore

Specificity

Quotes: "Small molecule identification, characterization, and procurement" and "Covers compound name to structure to activity to ADMET properties to commercial sourcing" list several concrete pipeline actions plus the specific tools (PubChem, ChEMBL, ADMET-AI, eMolecules, Enamine). It stops short of the score-5 anchor's comprehensive multi-action coverage (e.g., similarity/analog search, target prediction are not named), and it is well above the 1-2-action score-3 anchor.

4 / 5

Completeness

Both halves are explicit: the 'what' is the identification-to-procurement pipeline, and the 'when' is stated as "Use for chemical biology, lead identification, probe selection, and the full small-molecule discovery pipeline". The 'when' lists use-case domains rather than concrete user-trigger phrases (compare the score-5 example 'when the user mentions PDFs, forms'), so it matches the score-4 anchor: both present, 'when' could be more explicit.

4 / 5

Trigger Term Quality

Natural domain terms are present: "small molecule", "compound", "ADMET properties", "lead identification", "probe selection", "commercial sourcing", "chemical biology". Common user variations like "analog", "drug-likeness", "buy/availability", or "SMILES" are absent, so it fits the score-4 anchor (good coverage, a few natural terms missing) rather than the synonym- and extension-complete score-5 anchor.

4 / 5

Distinctiveness Conflict Risk

The niche is clear and distinct: small-molecule identification/characterization/procurement anchored to named chemistry resources (PubChem, ChEMBL, BindingDB, SwissADME, eMolecules, Enamine), which no adjacent skill (e.g., protein or document skills) would claim. It matches the score-5 anchor (clear niche with distinct triggers, minimal conflict risk) rather than the score-4 anchor's 'minor overlap risk with closely related skills'.

5 / 5

Total

17

/

20

Passed

Validation

100%

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

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
mims-harvard/ToolUniverse
Reviewed

Table of Contents

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