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glycoengineering

Analyzes and engineers protein glycosylation by scanning canonical N-glycosylation sequons, describing S/T-rich regions, checking curated glycan evidence, and preparing NetNGlyc, NetOGlyc and GlycoSHIELD workflows. Use for glycoprotein engineering, antibody Fc glycosylation, glycan shielding, and site-specific glycoproteomics interpretation.

72

Quality

91%

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SKILL.md
Quality
Evals
Security

Quality

Content

86%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-engineered skill body: executable, verified code examples; dense expert caveats rather than basics; and clean progressive disclosure into real, substantive reference files. The main improvement levers are consolidating the repeated motif-vs-occupancy caveats and adding explicit error-recovery guidance to the mutation workflow.

Suggestions

Consolidate the recurring 'motif does not establish occupancy' caveat into one clearly marked statement in the When-to-use section and trim its re-statements in the workflow and prediction sections.

Add a short fix-and-retry branch to the mutation workflow (e.g., what to do when the post-mutation rescan reveals a newly created overlapping sequon) to close the feedback-loop gap.

Trim the final verification-boundary paragraph to the two or three claims that are not already implied by the per-section scope statements.

DimensionReasoningScore

Conciseness

The body assumes domain competence (no basic glycosylation biology, no library tutorials) and packs in genuinely non-obvious caveats like "EU N297 is not residue 297 of an isolated Fc FASTA" and "shielding encoded in a PDB B-factor column; those values are not crystallographic temperature factors". It falls at 4 rather than 5 because the motif-vs-occupancy caveat is repeated across several sections and the closing verification-boundary section partially restates scope already signaled elsewhere, leaving minor trimming opportunities.

4 / 5

Actionability

Code examples are fully executable and copy-paste ready with real import instructions and runnable assertions (e.g., "assert [site['position'] for site in sites] == [1, 2]"), and every referenced function was verified to exist in scripts/glycoengineering_tools.py with matching signatures. The prediction table gives concrete thresholds and limits ("Default threshold 0.5", "Up to 2,000 sequences"), and the antibody table specifies exact mutations (N297Q/A/D, T299A) — matching the score-5 anchor.

5 / 5

Workflow Clarity

The 6-step workflow is clearly sequenced and includes explicit verification ("rescan the full product for lost/created overlapping motifs", "Verify the actual product", "Confirm occupancy, folding, binding and antigenicity"), so the batch/destructive cap does not apply. It sits at 4 rather than 5 because error-recovery feedback loops — what to do when a rescan or validation check fails — are not detailed; checkpoints are present but there is no fix-and-retry guidance.

4 / 5

Progressive Disclosure

The SKILL.md is a genuine overview with well-signaled, one-level-deep references — "Read [references/glycoshield.md] for the pinned source, installation, direct Python API" and "Read [references/glycan_databases.md] for the live GlyTouCan SPARQL lookup" — each prefaced with what it contains, and both files (plus both scripts) were verified to exist with matching content. Bulk detail is appropriately split out rather than inlined, matching the score-5 anchor.

5 / 5

Total

18

/

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, explicit what-and-when structure, and concrete capabilities that mirror the skill's sections. The only weakness is trigger-term breadth — a few natural synonyms and application phrasings (e.g., "glycosylation prediction", "glycoform", "ADCC") are missing.

Suggestions

Add one or two natural user phrasings such as "glycosylation site prediction" or "glycoform comparison" to the Use-for clause to widen trigger coverage.

DimensionReasoningScore

Specificity

"scanning canonical N-glycosylation sequons, describing S/T-rich regions, checking curated glycan evidence, and preparing NetNGlyc, NetOGlyc and GlycoSHIELD workflows" lists multiple concrete actions that map one-to-one onto the skill's major capability areas (local sequence analysis, prediction services, structural shielding, database evidence). This matches the score-5 anchor for comprehensive coverage of specific actions; it exceeds the 4 anchor because no major capability area is left uncovered.

5 / 5

Completeness

The description explicitly answers "what" (first sentence enumerating concrete capabilities) and "when" ("Use for glycoprotein engineering, antibody Fc glycosylation, glycan shielding, and site-specific glycoproteomics interpretation") with concrete trigger phrases, matching the score-5 anchor. It exceeds 4 because the "when" clause is explicit and specific rather than only serviceable.

5 / 5

Trigger Term Quality

"glycoprotein engineering, antibody Fc glycosylation, glycan shielding, and site-specific glycoproteomics interpretation" are natural phrases users in this domain would say, matching the 4 anchor (good keyword coverage, a few natural terms missing). It is not 5 because common variations such as "glycosylation site prediction", "Fc engineering", "glycoform", or "ADCC" are absent, and not 3 because the terms present are natural user language rather than jargon-only.

4 / 5

Distinctiveness Conflict Risk

"protein glycosylation" with triggers like "antibody Fc glycosylation" and "glycan shielding" carves out a clear niche with distinct trigger terms and minimal conflict risk with any plausible sibling skill, matching the score-5 anchor.

5 / 5

Total

19

/

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

K-Dense-AI/scientific-agent-skills

Path

skills/glycoengineering/SKILL.md

Reviewed

Table of Contents

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