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esm

Uses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding. Applies to local model inference and Biohub hosted clients, including former Forge workflows; distinguishes the separate legacy fair-esm distribution.

Quality

93%

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SKILL.md
Quality
Evals
Security

Quality

Content

92%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 dense, pitfall-aware guide with copy-paste-ready executable examples for all three SDK tasks, an explicit validated multi-step workflow, and a well-structured one-level-deep bundle in which every referenced file exists and is clearly signaled. The only soft spot is conciseness: inline version pins and date-stamped model identifiers, plus a lengthy citation protocol, leave minor room for trimming.

DimensionReasoningScore

Conciseness

Dense, pitfall-focused prose that assumes competence (no explanations of what proteins or embeddings are) and surfaces non-obvious facts like import-time token capture, "T is not the raw residue count", 1-based inclusive ranges, and the chain_id="all" default. It stops short of anchor 5 because time-sensitive details are inlined rather than isolated (version pins "esm==3.4.1.post1", date-stamped model IDs like "esmfold2-fast-2026-05") and the citation-fetching protocol is somewhat long — minor trims are possible, but not the padded over-explanation of anchor 3.

4 / 5

Actionability

Fully executable, copy-paste-ready guidance: exact install commands ("uv venv --python 3.12", "uv pip install ... esm==3.4.1.post1"), a task-to-model mapping table, and three complete code blocks with imports, model IDs, error checks, and asserts covering the three common cases (ESM3 generation, ESMC embeddings, hosted folding). Matches the top anchor.

5 / 5

Workflow Clarity

The five-step Workflow is clearly sequenced with explicit validation checkpoints — "Check every SDK result for ESMProteinError", "Validate the output contract: sequence length and fixed residues..." — plus input validation in step 1 ("Reject accidental `...`, spaces, FASTA headers or gaps"), all mirrored by isinstance/raise/assert checks in every code block. This matches the top anchor's explicit validation steps; the operations are non-destructive, so the batch-operation cap does not apply.

5 / 5

Progressive Disclosure

Verified against the actual bundle: every referenced file exists (references/forge-api.md, esm3-api.md, esm-c-api.md, biohub-platform.md, workflows.md, review.md, scripts/esm_embeddings.py), each link is well-signaled with its purpose (e.g., "See [ESM3](references/esm3-api.md) for inverse folding, function vocabulary and coordinate conventions"), and references are exactly one level deep — reference files link only to external sources, not to other bundle files. Clear overview with appropriately split content and easy navigation, matching the top anchor.

5 / 5

Total

19

/

20

Passed

Description

91%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 highly specific, well-scoped description that names all three concrete capability tracks, covers both local and hosted deployment, and explicitly disambiguates the legacy fair-esm distribution to avoid mis-triggering. The only weakness is that the "when" guidance is an "Applies to..." scope clause rather than an explicit "Use when..." trigger phrase tied to user situations, which costs it the top completeness score.

DimensionReasoningScore

Specificity

Lists multiple concrete capabilities — "ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding" — plus deployment modes ("local model inference and Biohub hosted clients"), comprehensively covering the SDK's three task tracks with no vague filler. Matches the top anchor (multiple specific concrete actions, comprehensive coverage) rather than anchor 4, which reserves room for coverage gaps.

5 / 5

Completeness

The "what" is explicit and concrete (the three capability tracks), and a "when" exists via "Applies to local model inference and Biohub hosted clients, including former Forge workflows" — an explicit scope clause, not a weak implication, so it sits above anchor 3. It falls short of anchor 5 because there is no "Use when..." style trigger phrasing tied to user situations (e.g., "when the user mentions protein sequences, ESM3, or ESMC embeddings").

4 / 5

Trigger Term Quality

Includes the natural terms a user would say when needing this skill — "esm", "ESM3", "ESMC", "ESMFold2", "protein generation", "embeddings", "all-atom folding" — plus synonyms for legacy contexts ("Forge", "fair-esm"). This mirrors the top anchor's comprehensive synonym coverage; no common domain phrasing is missing.

5 / 5

Distinctiveness Conflict Risk

Carves a clear niche (the Biohub esm SDK) and actively prevents mis-triggering by noting it "distinguishes the separate legacy fair-esm distribution" and covers "former Forge workflows". Clear niche with distinct triggers and minimal conflict risk, matching the top 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/esm/SKILL.md

Reviewed

Table of Contents

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