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ligandmpnn

Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al. 2023, github.com/dauparas/LigandMPNN). Reach for this skill to redesign the residues lining a binding pocket around a bound small molecule or cofactor, to design metal-coordinating sites where the geometry must be respected, or to get threaded designed-sequence PDBs out of any MPNN run.

78

Quality

100%

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

100%

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

A tightly written, highly actionable skill body: executable commands, a model-selection table, and several sharp failure-mode gotchas with concrete fixes. It balances conciseness with the depth needed for a fragile install/run path.

DimensionReasoningScore

Conciseness

Lean and dense; assumes Claude's competence (no re-explanation of what a PDB or MPNN is) and every section adds non-obvious gotchas rather than padding.

3 / 3

Actionability

Provides a fully executable install→clone→patch→fetch→run block with concrete flags, plus a copy-paste error-remediation table — copy-paste ready.

3 / 3

Workflow Clarity

Sequenced running steps and an explicit batch-output verification checkpoint ('If ligand_confidence... missing or zero... fix the input, do not trust the sequences') close the feedback loop for the batch inverse-folding operation.

3 / 3

Progressive Disclosure

No bundle files exist and none are needed; the single-purpose skill is cleanly sectioned (Running it, Model types, gotchas, Errors, Next) with no content that genuinely warrants splitting out.

3 / 3

Total

12

/

12

Passed

Description

100%

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 precise, well-scoped description that states concrete capabilities and gives explicit reach-for-this-skill trigger guidance in third-person voice. It avoids fluff and is clearly distinguishable from neighboring MPNN skills.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'redesign the residues lining a binding pocket', 'design metal-coordinating sites', 'get threaded designed-sequence PDBs' — matching the multiple-specific-actions anchor.

3 / 3

Completeness

Explicitly answers 'what' (inverse-fold with ligand/NA/metal context, threaded PDBs) and 'when' via the 'Reach for this skill to...' trigger clause, equivalent to a 'Use when' guidance.

3 / 3

Trigger Term Quality

Uses natural domain terms a structural-biology user would say ('binding pocket', 'metal-coordinating sites', 'ligand', 'cofactor', 'designed-sequence PDBs', 'LigandMPNN') with good coverage of variations.

3 / 3

Distinctiveness Conflict Risk

Clear niche — ligand-aware inverse folding — distinct from sibling proteinmpnn/solublempnn skills; written in third person, unlikely to trigger for the wrong skill.

3 / 3

Total

12

/

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.

Validation13 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

metadata_field

'metadata' should map string keys to string values

Warning

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

13

/

16

Passed

Repository
UnicomAI/wanwu
Reviewed

Table of Contents

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