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tooluniverse-binder-discovery

Discover novel small-molecule binders for protein targets using structure-based and ligand-based screening. Covers druggability assessment, known-ligand mining (ChEMBL, BindingDB), similarity expansion, ADMET filtering, and synthesis feasibility. Use for hit identification, virtual screening, target-to-compounds workflows, and lead-finding before commit-to-medchem.

Quality

90%

Does it follow best practices?

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SecuritybySnyk

Low

Low-risk findings worth noting

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.

An unusually actionable, well-sequenced workflow document rich in tool-specific detail Claude could not reproduce from memory, with only minor redundancy. The main structural defect is that all five declared reference files are missing from the bundle, breaking the progressive-disclosure chain and forcing the SKILL.md to inline detail that belongs in those files.

Suggestions

Ship the five referenced files (WORKFLOW_DETAILS.md, TOOLS_REFERENCE.md, REPORT_TEMPLATE.md, EXAMPLES.md, CHECKLIST.md) in the skill bundle, or remove the links and keep the essential content inline — currently every reference link dangles.

Move the inlined Fallback Chains block, Programmatic Access code, and NVIDIA NIM Runtime Notes into TOOLS_REFERENCE.md / WORKFLOW_DETAILS.md so SKILL.md stays a true overview.

State the NVIDIA_API_KEY requirement once (e.g., in a single 'NVIDIA NIM prerequisites' note) instead of repeating it parenthetically in Phase 0, Phase 1.4, and Phase 3.5, and merge the duplicated AlphaFold2/ESMFold timing details.

DimensionReasoningScore

Conciseness

The body is dense with tool-specific facts Claude cannot know (parameter quirks like 'sequence not seq', API-key requirements, thresholds like 'IC50/Ki/Kd < 10 uM', evidence tiers), so most tokens earn their place. Minor trimming opportunities: the NVIDIA_API_KEY requirement is stated three times (Phase 0, Phase 1.4, Runtime Notes), ESMFold/AlphaFold timings appear in both Phase 1.4 and Runtime Notes, and the Binding Site Reasoning section partially re-explains structural biology Claude already knows.

4 / 5

Actionability

Highly actionable throughout: exact tool names with parameter signatures (`ChEMBL_search_similar_molecules(query=SMILES, similarity_threshold=70)`), concrete numeric cutoffs (QED > 0.3, MW 200-600, AMES < 0.5), a copy-paste-ready Python block for direct PubChem/ChEMBL API access, GenMol mask syntax, and a fully specified composite scoring formula. The common cases are covered with executable examples.

5 / 5

Workflow Clarity

Phases 0-7 are clearly sequenced with explicit validation checkpoints: Phase 0 verifies tool parameters before use, Phase 3.5 docks a reference inhibitor to validate pocket geometry before candidate docking, a 'Decision Point' gates proceeding on poor tractability, fallback chains provide error-recovery loops, and a CHECKLIST reference supports pre-delivery verification. Batch expansion even includes chunking guidance for >500 compounds.

5 / 5

Progressive Disclosure

The structure is well signaled — five one-level-deep reference links at the end, each labeled with its purpose — but none of the referenced files (WORKFLOW_DETAILS.md, TOOLS_REFERENCE.md, REPORT_TEMPLATE.md, EXAMPLES.md, CHECKLIST.md) exist in the bundle, so the navigation leads nowhere. Additionally, content that the reference files should own (fallback chains, direct-API code, NIM runtime notes) is inlined in SKILL.md.

3 / 5

Total

17

/

20

Passed

Description

92%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: third-person voice, dense with concrete capabilities, and an explicit 'Use for...' clause with realistic trigger terms. The only gap is a few missing natural synonyms (e.g., 'find inhibitors', 'docking') that users might phrase differently.

DimensionReasoningScore

Specificity

The description lists multiple specific concrete actions covering the full workflow: "Discover novel small-molecule binders for protein targets using structure-based and ligand-based screening", "druggability assessment, known-ligand mining (ChEMBL, BindingDB), similarity expansion, ADMET filtering, and synthesis feasibility". This matches the anchor for comprehensive coverage of concrete actions; nothing is vague or padded.

5 / 5

Completeness

Both questions are answered explicitly: the 'what' ("Discover novel small-molecule binders... Covers druggability assessment, known-ligand mining...") and a concrete 'when' ("Use for hit identification, virtual screening, target-to-compounds workflows, and lead-finding before commit-to-medchem"). This mirrors the top anchor with concrete trigger phrases.

5 / 5

Trigger Term Quality

Good natural-keyword coverage: "hit identification", "virtual screening", "target-to-compounds workflows", "lead-finding", "small-molecule binders" — phrases a drug-discovery user would actually say. A few common synonyms are missing (e.g. "find inhibitors for [target]", "docking", "ligand discovery"), which fits the 'good coverage, a few natural terms missing' anchor rather than the comprehensive one.

4 / 5

Distinctiveness Conflict Risk

A clear niche (ToolUniverse-based binder discovery) with distinct domain triggers, and the scope boundary "before commit-to-medchem" explicitly separates it from adjacent medchem skills. Conflict risk with generic skills is minimal.

5 / 5

Total

19

/

20

Passed

Validation

93%

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

Validation — 15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

relative_links

Relative link issues: 5 missing

Warning

Total

15

/

16

Passed

Repository

mims-harvard/ToolUniverse

Path

plugin/skills/tooluniverse-binder-discovery/SKILL.md

Reviewed

Table of Contents

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