Conciseness

The body is dense with non-obvious operational content (CLI flags, modes, gotchas like DPP4 liability, Hemolytik2/PEPlife2 enum limits, the live-broken ConoServer), assuming Claude's competence throughout. Minor trimming is possible: the validated-control result is stated twice (in the script section and again under 'Validation & test'), and the 'not just GPCRs' premise is restated several times. This fits 'efficient; minor instances of over-explanation' better than the level-3 anchor, since most tokens earn their place.

Actionability

Both scripts have full bash invocations with all flags explained, a runnable validated control command with a real sequence, and clearly defined modes and output tiers. It falls short of fully copy-paste-ready, though: the main deorphanize_peptide.py block embeds '#' comments on backslash-continuation lines (invalid bash if pasted), and the per-phase manual calls are deferred to references/phases.md rather than shown. Anchor 4 ('mostly executable guidance; concrete code or commands with minor gaps') is the best fit.

Workflow Clarity

The six-phase pipeline is clearly sequenced in a table mapped to scripts and key tools, with explicit validation checkpoints (Phase 0 tool verification, key-gated dry-run mode, eval assertions for regression) and feedback loops for error recovery (fallback chains when a tool fails, 'degrades to phenotype-only if that resolver is transiently down', insufficient-data handling for protists missing from UniProt). Batch mode has no destructive risk and is covered by the eval checks. This matches the top anchor: clear sequence, explicit validation, error-recovery guidance.

Progressive Disclosure

Good structure: SKILL.md is a genuine overview with clearly signaled, well-motivated one-level-deep references ('read it when a script step fails, when you want to drive a phase manually...') to references/phases.md, and both referenced scripts exist in the bundle. The gap keeping it below the top anchor: the body points to 'evals/evals.json' for reproducible test prompts, but no evals/ directory exists in the bundle — a dangling reference — and the ~25-line supplementary database table is borderline inline material that could live in a reference file.

Specificity

"Find the real protein target(s) of a peptide from its sequence — peptide target deorphanization / off-target identification" plus "screen candidate targets for an orphan peptide" lists multiple concrete actions, and the pipeline enumeration (PROSITE/ELM motif, BLAST homology, target-family enumeration, phenotype anchor, cross-species reconciliation, co-folding) gives comprehensive, explicitly stated coverage. This matches the top anchor; the level-4 anchor ('minor gaps in coverage') does not apply since every major capability of the pipeline is named.

Completeness

What is answered explicitly ("Find the real protein target(s) of a peptide from its sequence", for "ANY target class (GPCR, ion channel, protease, cytokine/growth-factor receptor, enzyme, integrin), not only GPCRs") and when is answered with an explicit "Use when..." clause listing three concrete trigger scenarios. This matches the top anchor exactly; anchor 4 ('when could be more explicit or specific') is clearly below what is present.

Trigger Term Quality

Natural phrases a user would actually say are present verbatim: "peptide has a phenotype but does not bind its hypothesized target", "binds a target in one species or assay but not another", "orphan peptide", "off-target identification", "deorphanization". These cover the common synonyms for this need; the score-4 anchor ('a few natural terms missing') is not met — even species-mismatch and negative-assay phrasings are included.

Distinctiveness Conflict Risk

"Peptide target deorphanization / off-target identification" is a clear niche with distinct triggers (orphan peptide, hypothesized-target negative, species-mismatch binding) and a named tool pipeline; minimal overlap risk with any generic bioinformatics or peptide-property skill. No neighboring anchor fits better.