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brenda-database

Retrieve enzyme kinetic data from the BRENDA SOAP API using Python.

1|Updated Mar 11, 2026
Search Tags:#bioinformatics#kcat#enzyme#brenda#soap#km#reaction
One-click install
npx skills add https://github.com/SciMate-AI/scicli --skill brenda-database-scimate-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: brenda-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/brenda-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill brenda-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Access to enzyme data from the BRENDA SOAP API to retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific information for biochemical research and metabolic analysis.

Core Features & Use Cases

  • Retrieve Km values across organisms and substrates using get_km_values with optional organism and substrate filters.
  • Retrieve reactions and organisms for enzymes via get_reactions, with parsing utilities to extract substrates/products.
  • Compare enzyme properties across organisms, environmental parameters, and substrate specificity to support pathway design and enzyme engineering.
  • Use cases: cross-organism enzyme comparison, pathway construction, and data-driven enzyme selection for metabolic engineering.

Quick Start

Run a Km data query for EC 1.1.1.1 across organisms and view summarized results.

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 Km values from the BRENDA database for cross-organism comparison?▼

Retrieve enzyme Km values from the BRENDA database using the get_km_values function, which supports optional organism and substrate filters to facilitate cross-organism comparisons and metabolic analysis.

Can I query BRENDA enzyme reactions and parse specific substrates and products?▼

Query BRENDA enzyme reactions using the get_reactions function, which includes parsing utilities to extract specific substrates and products for pathway construction and metabolic engineering applications.

Do I need Python and the zeep library to access the BRENDA SOAP API for enzyme data?▼

Accessing the BRENDA SOAP API requires Python along with the zeep, requests, and pandas libraries to retrieve kinetic parameters like kcat and Km values for biochemical research.

Does the BRENDA API query support wildcard EC numbers and organism filters?▼

The BRENDA API query supports wildcard EC numbers, organism filters, and substrate filters to retrieve specific enzyme data for cross-organism comparisons and reaction queries.

What is the best way to compare enzyme kinetic parameters like kcat and Km across different organisms?▼

Compare enzyme kinetic parameters like kcat and Km across organisms by retrieving data via the BRENDA SOAP API, then using pandas to parse and summarize results for data-driven enzyme selection.

Why use BRENDA SOAP API over other methods for retrieving enzyme kinetic data?▼

Use the BRENDA SOAP API to directly retrieve comprehensive enzyme kinetic data, including kcat and Km values, reaction equations, and organism-specific information for biochemical research and pathway analysis.

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