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boltz

Structure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al. 2025, github.com/jwohlwend/boltz). Reach for this skill to validate designed binders against a target, to co-fold a protein with a SMILES or CCD ligand, or to get an open-source AlphaFold3 alternative with optional binding-affinity prediction.

73

Quality

93%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

SKILL.md
Quality
Evals
Security

Quality

Content

87%

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

The body is lean, actionable, and well-organized with executable examples and a useful error table. Its main gap is the lack of an explicit validation checkpoint / feedback loop in the run workflow, which is the one dimension that falls short of full marks.

Suggestions

Add a short numbered run workflow with an explicit checkpoint after `boltz predict` (e.g. "Verify `confidence_complex_model_0.json` exists and `iptm`/`complex_plddt` meet thresholds before ranking models; if absent or low, re-run with `--use_msa_server` or more `--diffusion_samples`").

Frame the error-recognition table as an explicit fix→retry loop so failed runs route back to a corrective action and re-run rather than just listing symptoms.

Surface the OOM and fast-kernel fallbacks as a single ordered triage step (check VRAM → lower `--diffusion_samples`/`--max_parallel_samples` → `--no_kernels`) so recovery has a clear sequence.

DimensionReasoningScore

Conciseness

Dense and high-value throughout, assuming domain competence (e.g. "`iptm` > 0.5 is the community pass line", "log10(IC50 in μM) — lower is tighter (≈0 → 1 μM, −3 → 1 nM)") with no padding of concepts Claude already knows.

3 / 3

Actionability

Provides a complete `complex.yaml` and a copy-paste `boltz predict` command with real flags, plus concrete output paths and decision thresholds — fully executable rather than pseudocode.

3 / 3

Workflow Clarity

The happy path (YAML → predict → read confidence JSON → check thresholds) and an error table are present, but there is no explicit validate→fix→retry checkpoint sequence, which the feedback-loops note expects for a long-running batch/prediction operation.

2 / 3

Progressive Disclosure

No bundle files exist; the single self-contained SKILL.md is well-sectioned (Running it, Affinity head, accuracy-vs-memory, fast kernels, Errors) with one-level, clearly signaled cross-references, satisfying the simple-skills note.

3 / 3

Total

11

/

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.

The description is specific, complete, and well-triggered, naming concrete capabilities and explicit use-conditions in third person. It distinguishes the skill clearly from neighboring co-folders.

DimensionReasoningScore

Specificity

Enumerates several concrete actions — "validate designed binders against a target", "co-fold a protein with a SMILES or CCD ligand", and "binding-affinity prediction" — matching the multiple-specific-actions anchor.

3 / 3

Completeness

Explicitly states what ("Structure prediction for protein, nucleic-acid, and small-molecule complexes") and when ("Reach for this skill to validate designed binders... or to get an open-source AlphaFold3 alternative"), satisfying both halves with an explicit trigger clause.

3 / 3

Trigger Term Quality

Uses natural terms a structural-biology user would actually say ("validate designed binders", "co-fold", "AlphaFold3 alternative", "binding-affinity prediction"), with only minor plain-language variants absent.

3 / 3

Distinctiveness Conflict Risk

Occupies a clear Boltz-2 co-folding niche with distinct triggers and is explicitly differentiated from sibling co-fold skills, making a wrong-skill trigger unlikely.

3 / 3

Total

12

/

12

Passed

Validation

75%

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

Validation12 / 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

relative_links

Relative link issues: 1 missing

Warning

Total

12

/

16

Passed

Repository
UnicomAI/wanwu
Reviewed

Table of Contents

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