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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).

72

Quality

88%

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SKILL.md
Quality
Evals
Security

Quality

Content

82%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 lean, actionable skill body with executable commands, real bundle references, and a well-sequenced workflow that includes quality checkpoints and gotchas. Minor gains are available from tightening basic parameter explanations and adding an explicit validation retry loop.

Suggestions

Trim basic kinetic definitions (e.g. 'lower Km = tighter binding', 'apparent affinity') that Claude already knows, keeping only tool-specific interpretation notes.

Add an explicit validate-and-retry feedback loop, e.g. after the fit: 'If residuals show systematic curvature or R²<0.98, do not report Km/Vmax — widen the [S] range or consider substrate inhibition / a Hill model.'

Consider moving the full parameter and inhibition-mode reference tables into a references/ file referenced one level deep, keeping SKILL.md as a tighter overview.

DimensionReasoningScore

Conciseness

Mostly efficient with task-specific interpretation tables and a pointed Lineweaver-Burk warning that earns its place; minor over-explanation of basic parameter meanings (e.g. 'lower Km = tighter binding') that could be trimmed since Claude already knows MM kinetics.

4 / 5

Actionability

Fully executable copy-paste-ready `tu run EnzymeKinetics_calculate` commands with concrete argument values for both the michaelis_menten and inhibition operations, plus a real referenced script (`scripts/fit_michaelis_menten.py`) that exists in the bundle.

5 / 5

Workflow Clarity

Clear five-step sequence (Prepare → Fit → Interpret → Inhibition → Gotchas) with quality checkpoints (R²≥0.98, residual-curvature check, Km-in-range trustworthiness) and error-recovery cues (flag substrate inhibition rather than forcing a fit); not a full 5 because there is no explicit validate-then-retry feedback loop.

4 / 5

Progressive Disclosure

Well-organized sections with a clearly signaled one-level-deep reference to a real bundle file (`scripts/fit_michaelis_menten.py`) and a related-skills pointer; the detailed parameter and inhibition tables are concise enough to live inline, though a dedicated reference file could carry the fuller interpretation guidance.

4 / 5

Total

17

/

20

Passed

Description

95%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, specific description that clearly states capabilities, trigger conditions, and a disambiguation boundary against the BRENDA lookup skill. The only weakness is second-person phrasing in the trigger clause.

Suggestions

Rephrase the trigger to third person to match the rubric's voice requirement, e.g. 'Use when substrate concentrations and initial reaction velocities are available and kinetic parameters or inhibitor classification are needed.'

DimensionReasoningScore

Specificity

Lists multiple concrete actions (Km/Vmax/kcat/kcat/Km from substrate-velocity data, inhibition-mechanism analysis with three modes + Ki, nonlinear regression fit) with comprehensive coverage; docked one point because the trigger clause 'Use when you have...' uses second-person voice, which the rubric penalizes.

4 / 5

Completeness

Explicitly answers both what (computes Km/Vmax/kcat/kcat/Km and classifies inhibition mechanism) and when ('Use when you have substrate concentrations and initial reaction velocities and need kinetic parameters or to classify an inhibitor') with concrete trigger phrases.

5 / 5

Trigger Term Quality

Comprehensive natural terms a practitioner would say — 'enzyme kinetics', 'Michaelis-Menten', 'Km', 'Vmax', 'kcat', 'substrate', 'velocity', 'inhibitor' — plus synonyms ('catalytic efficiency / specificity constant') and the three inhibition modes.

5 / 5

Distinctiveness Conflict Risk

Clear niche (Michaelis-Menten enzyme kinetics on measured data) with an explicit boundary — 'NOT for BRENDA database lookups of published constants (use the BRENDA tools)' — minimizing conflict with the sibling BRENDA skill.

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.

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
mims-harvard/ToolUniverse
Reviewed

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