brenda-database

Retrieve enzyme kinetic parameters and reaction data from the BRENDA database via SOAP API.

1|Updated Jan 14, 2026
One-click install
npx skills add https://github.com/Sologa/codex-pipeline --skill brenda-database-sologa
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: brenda-database
Source: https://github.com/Sologa/codex-pipeline/tree/main/.codex/skills/brenda-database
Command: npx skills add https://github.com/Sologa/codex-pipeline --skill brenda-database-sologa

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires zeep, requests, pandas, matplotlib, seaborn, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides programmatic access to the BRENDA enzyme database, enabling researchers to retrieve detailed enzyme kinetic parameters, reaction information, and organism-specific data, thereby accelerating biochemical research and pathway analysis.

Core Features & Use Cases

  • Kinetic Parameter Retrieval: Access Km, kcat, and Vmax values for enzymes.
  • Reaction Information: Retrieve detailed reaction equations and stoichiometry.
  • Enzyme Discovery: Find enzymes based on substrates, products, or reaction patterns.
  • Organism-Specific Data: Compare enzyme properties across different species.
  • Use Case: A metabolic engineer needs to find enzymes that can convert glucose to pyruvate in E. coli with high catalytic efficiency. This Skill can query BRENDA for relevant enzymes, filter by organism and substrate, and rank them by kinetic parameters.

Quick Start

Use the brenda-database skill to get Km values for alcohol dehydrogenase (EC 1.1.1.1).

Frequently Asked Questions about brenda-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve enzyme kinetic parameters like Km and kcat from the BRENDA database?

You retrieve enzyme kinetic parameters from the BRENDA database by querying specific EC numbers via a SOAP API. The Skill parses and returns structured Km, kcat, and Vmax values along with their associated environmental conditions for comprehensive biochemical research.

Can I find organism-specific enzyme data and substrate specificities using a SOAP API?

Yes, you can retrieve organism-specific enzyme data and substrate specificities using the BRENDA SOAP API. It facilitates filtering by organism and substrate to compare enzyme properties across different species for metabolic pathway analysis.

What's the best way to access BRENDA enzyme reaction equations and stoichiometry programmatically?

The best way to access BRENDA enzyme reaction equations and stoichiometry programmatically is through this SOAP API integration. It provides structured access to millions of data points for over 45,000 enzymes, parsing detailed reaction information for metabolic engineering.

Do I need authentication credentials to query BRENDA enzyme data?

Yes, you need authentication credentials to query BRENDA enzyme data via the SOAP API. The Skill requires these credentials to access and retrieve comprehensive enzyme kinetic parameters, reaction equations, and organism-specific data for your research.

How do I analyze metabolic pathways by ranking enzymes based on catalytic efficiency?

You analyze metabolic pathways by querying BRENDA for relevant enzymes, filtering by organism and substrate, and ranking them by kinetic parameters. This identifies enzymes with high catalytic efficiency for specific biochemical conversions in metabolic engineering.