brenda-database
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
npx skills add majiayu000/claude-skill-registry --skill brenda-database-sologa-codex-pipeline --agent codex
Same command for any agent — swap --agent for claude-code, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
What it does
The skill provides a set of Python-guided procedures to access the BRENDA enzyme database through a SOAP API, enabling retrieval of kinetic parameters (Km, kcat), reaction equations, organism data, substrate-specific information, and related enzyme details for biochemical research and pathway analysis.
How it works
It includes concrete code examples and function descriptions that:
- Get Km values by EC number, optionally filtered by organism or substrate.
- Parse and extract organism, substrate, Km, pH, and temperature from Km entries.
- Retrieve reactions by EC number, with optional organism filter or specific reaction query, and process substrates/products.
- Discover enzymes by substrate, product, or reaction pattern, returning EC numbers, names, and reactions.
- Compare enzyme data across organisms for a given EC number, including average Km, optimal pH, and temperature.
- Get organism-specific enzyme data and identify organisms possessing a given enzyme.
- Access environmental parameters such as pH range, optimal temperature, and stability metrics, plus cofactor requirements.
- Analyze substrate specificity and compare substrate affinities across substrates.
- Retrieve inhibition and activation data for regulation, and explore engineering targets like thermophilic homologs and pH-stable variants.
- Prepare data for kinetic modeling and generate Michaelis–Menten plots.
- Include a comprehensive set of helper scripts and plotting utilities for data export and visualization.
When to use it
Use this skill when:
- You need kinetic parameters (Km, kcat, Vmax) for enzymes (EC numbers).
- You require reaction equations, substrate specifics, or organism context.
- You are searching for enzymes related to a specific substrate, product, or reaction pattern.
- You want to compare enzyme properties across organisms or analyze environmental conditions.
- You are building metabolic pathways, retrosynthetic routes, or performing enzyme engineering analyses.
- You intend to model enzyme kinetics and generate visualizations.
What it can touch
- Functions and scripts under scripts/brenda_queries.py and scripts/brenda_visualization.py for querying and plotting.
- Visualization routines like plot_michaelis_menten used to generate kinetic curves.
Caveats
- License is listed as Unknown in the front matter and the repository metadata.
- API usage is subject to rate limits and authentication setup, including environment variables or a .env file for BRENDA credentials.
- Uses external dependencies (e.g., zeep, requests, pandas, matplotlib) and assumes proper API access and data availability.
# BRENDA Database ## Overview BRENDA (BRaunschweig ENzyme DAtabase) is the world's most comprehensive enzyme information system, containing detailed enzyme data from scientific literature. Query kinetic parameters (Km, kcat), reaction equations, substrate specificities, organism information, and optimal conditions for enzymes using the official SOAP API. Access over 45,000 enzymes with millions of kinetic data points for biochemical research, metabolic engineering, and enzyme discovery. ## When to Use This Skill This skill should be used when: - Searching for enzyme kinetic parameters (Km, kcat, Vmax) - Retrieving reaction equations and stoichiometry - Finding enzymes for specific substrates or reactions - Comparing enzyme properties across different organisms - Investigating optimal pH, temperature, and conditions - Accessing enzyme inhibition and activation data - Supporting metabolic pathway reconstruction and retrosynthesis - Performing enzyme engineering and optimization studies - Analyzing substrate specificity and cofactor requirements ## Core Capabilities ### 1. Kinetic Parameter Retrieval Access comprehensive kinetic data for enzymes: **Get Km Values by EC Number**: ```pyt
- Overview
- When to Use This Skill
- Core Capabilities
- 1. Kinetic Parameter Retrieval
- 2. Reaction Information
- 3. Enzyme Discovery
- 4. Organism-Specific Enzyme Data
- 5. Environmental Parameters
- 6. Substrate Specificity
- 7. Inhibition and Activation
- 8. Enzyme Engineering Support
- 9. Kinetic Modeling
- Installation Requirements
- Authentication Setup
uv pip install zeep requests pandas matplotlib seaborn export BRENDA_EMAIL="your.email@example.com" export BRENDA_PASSWORD="your_brenda_password"
What does the brenda-database skill do?
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill brenda-database-sologa-codex-pipeline --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.