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tooluniverse-enzyme-kinetics

Enzyme kinetics — Michaelis-Menten Km, Vmax, kcat (turnover), and kcat/Km (catalytic efficiency / specificity constant) from substrate-velocity data, plus inhibition-mechanism analysis (competitive / uncompetitive / non-competitive, Ki). Fits the MM equation by nonlinear regression (and reports Lineweaver-Burk for reference). Use when you have substrate concentrations and initial reaction velocities and need kinetic parameters or to classify an inhibitor. NOT for BRENDA database lookups of published constants (use the BRENDA tools).

76

Quality

95%

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SecuritybySnyk

Passed

No findings from the security scan

The canonical home for this skill is tooluniverse-enzyme-kinetics in mims-harvard/ToolUniverse

SKILL.md
Quality
Evals
Security

Quality

Content

88%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 strong, highly actionable skill body: executable commands with realistic data, a real supporting script, sequenced steps with validation checkpoints and recovery guidance, and an honest limitations section. The main trim opportunities are the textbook definitions in the Step 3 table, duplicated Lineweaver-Burk/kcat warnings between Steps 1–2 and Step 5, and the inlined SABIO-RK lookup section.

Suggestions

Drop the 'Meaning' column of the Step 3 table (Km/kcat/kcat-Km definitions are textbook knowledge Claude already has) and keep only the skill-specific 'Notes' column to cut redundant explanation.

State the Lineweaver-Burk caution once (the Step 2 blockquote) and remove the duplicate gotcha in Step 5; likewise the kcat-requires-[E] point already appears in the Step 1 table.

Reduce the SABIO-RK section to a one-line pointer (or move it to a reference file) since it documents a lookup tool this skill explicitly disclaims, and reference scripts/fit_michaelis_menten.py in a clearly signaled section so the bundle file is easy to discover.

DimensionReasoningScore

Conciseness

Mostly dense and efficient — compact tables, copy-paste commands, no library-selection padding — but the Step 3 'Meaning' column restates textbook definitions Claude already knows ('Km: substrate concentration at ½Vmax', 'kcat: Turnover number = Vmax/[E]'), and the Lineweaver-Burk caution and the kcat-requires-[E] point are each stated twice (Step 2 blockquote + Step 5 gotchas; Step 1 table + Step 5 gotchas). Not 5: these redundancies and the inlined ~10-line SABIO-RK section are tokens that could be trimmed; not 3: the over-explanation is minor and the skill-specific notes (R²≥0.98, ~0.2×–5×Km range, diffusion-limit benchmark) genuinely earn their place.

4 / 5

Actionability

Fully executable: 'tu run EnzymeKinetics_calculate' with a realistic numeric payload for the common case, named-field example for the inhibition operation, concrete thresholds (≥5–7 points, ~0.2×Km to ~5×Km, R²≥0.98, <10% substrate consumed), and a real bundled script (scripts/fit_michaelis_menten.py, verified present) with CSV usage and kcat conversion. Not 4: there is no gap — even edge handling (empty parameters array in SABIO-RK) comes with a concrete remedy.

5 / 5

Workflow Clarity

Steps 1–5 are clearly sequenced (prepare → fit → interpret → inhibition → gotchas) with explicit validation checkpoints and recovery loops: check residuals for systematic curvature (pattern means MM is the wrong model), Km must lie inside the tested range → widen [S], substrate inhibition → flag instead of forcing one Km, and the gotchas section is an explicit 'state these' checklist. Not 4: validation and error-recovery guidance is present at every stage, matching the anchor's validate→fix→retry pattern.

5 / 5

Progressive Disclosure

Good structure for a single-file skill: well-organized sections, and the sole bundle file (scripts/fit_michaelis_menten.py) is referenced inline with an accurate one-line description and verified to exist. Not 5: the ~10-line SABIO-RK lookup section (an adjacent tool the skill explicitly disclaims) is inlined mid-workflow rather than split out or reduced to a pointer, and the bundle script is mentioned in passing rather than clearly signaled as part of the bundle structure; not 3: the core fitting content is appropriately placed and navigable.

4 / 5

Total

18

/

20

Passed

Description

100%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.

An exemplary description: concrete third-person capabilities, comprehensive natural trigger vocabulary with synonyms, explicit what-and-when clauses, and a stated negative boundary that separates it from adjacent lookup and dose-response skills. It closely matches the rubric's good-overall examples in structure and density.

DimensionReasoningScore

Specificity

Lists multiple specific concrete actions with comprehensive coverage: deriving 'Michaelis-Menten Km, Vmax, kcat (turnover), and kcat/Km (catalytic efficiency / specificity constant) from substrate-velocity data', 'inhibition-mechanism analysis (competitive / uncompetitive / non-competitive, Ki)', and 'Fits the MM equation by nonlinear regression (and reports Lineweaver-Burk for reference)' — all in third person. Not 4: there are no minor coverage gaps; parameters, mechanisms, fit method, and reported outputs are all named.

5 / 5

Completeness

Explicitly answers both questions: the first sentences state what ('Fits the MM equation by nonlinear regression', derives Km/Vmax/kcat/kcat/Km and inhibition mode + Ki) and 'Use when you have substrate concentrations and initial reaction velocities and need kinetic parameters or to classify an inhibitor' gives concrete when-triggers. Not 4: the 'when' clause is fully explicit, not merely present; a bonus negative boundary ('NOT for BRENDA database lookups') sharpens it further.

5 / 5

Trigger Term Quality

Comprehensive natural keywords a biochemist would actually say — 'enzyme kinetics', 'Michaelis-Menten', 'Km', 'Vmax', 'kcat', 'inhibitor', 'Ki', 'substrate concentrations', 'initial reaction velocities', 'BRENDA' — with synonyms included ('turnover' for kcat, 'catalytic efficiency / specificity constant' for kcat/Km) and all three inhibition modes enumerated. Not 4: no common variation is missing; synonym coverage matches the anchor-5 pattern.

5 / 5

Distinctiveness Conflict Risk

Clear niche (analyzing one's own measured substrate-velocity data) with distinct parameter triggers (Km/Vmax/kcat) that adjacent skills (dose-response IC50/EC50, BRENDA lookups) would not fire on, plus an explicit 'NOT for BRENDA database lookups of published constants (use the BRENDA tools)' boundary. Not 4: the overlap-prone neighbor is explicitly disambiguated, leaving minimal conflict risk.

5 / 5

Total

20

/

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
mims-harvard/ToolUniverse
Reviewed

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