Skills brenda-database

brenda-database

Name: brenda-database
Author: K-Dense-AI

Low Risk 🌐 Network access📁 Filesystem access⚡ Contains scripts

Query enzyme data from BRENDA database

Also available from: davila7

Access comprehensive enzyme kinetic data from the worlds largest enzyme database. Find Km values, reaction equations, organism-specific parameters, and substrate specificity data for biochemical research and metabolic engineering.

Supports: Claude Codex Code(CC)

📊 71 Adequate

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Test it

Using "brenda-database". Get Km values for alcohol dehydrogenase (EC 1.1.1.1) for human and yeast

Expected outcome:

Alcohol Dehydrogenase (EC 1.1.1.1) Kinetic Data:
Homo sapiens:
- Average Km: 0.34 mM (ethanol)
- Optimal pH: 8.0-9.0
- Temperature: 25C (data points: 15)
Saccharomyces cerevisiae:
- Average Km: 1.2 mM (ethanol)
- Optimal pH: 7.0-8.0
- Temperature: 30C (data points: 8)
Cofactors: NAD+ required for both organisms

Security Audit

Low Risk

v4 • 1/17/2026

The brenda-database skill is a legitimate scientific tool for accessing enzyme data from the BRENDA database. All 436 static findings are false positives triggered by documentation formatting (backtick characters for code blocks), legitimate BRENDA API authentication (SHA-256 password hashing), and biochemical terminology (NAD+, ATP as cofactors, not C2 commands). The codebase performs authorized SOAP API queries to a public scientific database and exports research data. No malicious behavior, data exfiltration, or unauthorized access patterns were found.

Files scanned

4,388

Lines analyzed

findings

Total audits

Risk Factors

🌐 Network access (1)

references/api_reference.md:10-12

📁 Filesystem access (1)

scripts/brenda_queries.py:756-766

⚡ Contains scripts (1)

scripts/brenda_queries.py:33-64

Audited by: claude View Audit History →

Quality Score

Architecture

100

Maintainability

Content

Community

Security

Spec Compliance

What You Can Build

Enzyme kinetic analysis

Retrieve Km and kcat values to characterize enzyme behavior and compare across organisms.

Pathway design

Find enzymes for specific reactions and optimize conditions for metabolic pathway construction.

Literature data extraction

Extract enzyme parameters from published BRENDA data for computational modeling and analysis.

Try These Prompts

Basic query

Get Km values for alcohol dehydrogenase (EC 1.1.1.1) from BRENDA.

Organism filter

Find Km values for EC 1.1.1.1 in Escherichia coli and Homo sapiens.

Reaction search

Find all reactions involving glucose and their enzyme EC numbers.

Pathway builder

Find the enzymatic pathway to produce lactate from pyruvate including all required cofactors.

Best Practices

Store BRENDA credentials in environment variables for secure authentication
Add rate limiting delays (0.5-1 second) between API calls to avoid rate limits
Use specific EC numbers and organism filters to reduce data volume and improve response times

Avoid

Making concurrent API requests without delays will trigger rate limiting
Using wildcards for broad searches without limiting results can return massive datasets
Not caching results for repeated queries wastes API quota and slows performance