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brenda-database

Retrieve enzyme kinetic data from the BRENDA SOAP API by EC number and organism.

4|1|Updated Jun 18, 2025
Search Tags:#reactions#brenda#soap-api#km-values#enzyme-database#environmental-parameters#cofactors
One-click install
npx skills add https://github.com/HolobiomicsLab/Toolomics --skill brenda-database-holobiomicslab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: brenda-database
Source: https://github.com/HolobiomicsLab/Toolomics/tree/main/mcp_host/skills/scientific-skills/scientific-skills/brenda-database
Command: npx skills add https://github.com/HolobiomicsLab/Toolomics --skill brenda-database-holobiomicslab

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Access to the BRENDA enzyme database via the SOAP API for programmatic retrieval of kinetic parameters (Km, kcat), reactions, organism-specific data, and substrate information to accelerate biochemical research and enzyme discovery.

Core Features & Use Cases

  • Retrieve Km values for enzymes and compare across organisms or substrates.
  • Discover reactions and substrate specificity to map metabolic capabilities.
  • Extract environmental parameters and cofactor requirements for pathway design and modeling.
  • Build workflows for enzyme discovery, pathway planning, and kinetic analysis.

Quick Start

Query Km values for EC 1.1.1.1 across organisms and review environmental parameters.

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 SOAP API for multiple organisms?▼

Retrieve enzyme Km values by querying the BRENDA SOAP API with a specific EC number and target organisms. The Skill manages data parsing, authentication, and rate limiting, enabling robust cross-organism comparisons for biochemical research.

What enzyme data fields can I extract using the BRENDA SOAP API?▼

You can extract Km values, kcat kinetic parameters, reactions, substrate specificity, environmental parameters, and cofactor requirements. These fields support metabolic mapping and pathway design by detailing enzyme functional capabilities across different organisms.

Does this Skill handle API rate limiting and missing optional data fields from BRENDA?▼

Yes, the Skill implements robust error handling and rate limiting for the BRENDA SOAP API. It includes data parsing utilities that support optional data fields, ensuring successful queries even when specific kinetic or environmental parameters are missing.

Can I map metabolic pathways using enzyme substrate specificity and cofactor data?▼

Yes, you can map metabolic capabilities by extracting substrate specificity and cofactor requirements. The Skill retrieves this data to enable pathway planning, allowing researchers to model reactions and evaluate environmental parameters across target organisms.

What is the best way to programmatically compare enzyme kinetic parameters across organisms?▼

The best way is querying the BRENDA SOAP API with an EC number and organism list. This Skill parses returned kinetic parameters, like Km values, into structured formats, enabling direct cross-organism comparisons for enzyme discovery workflows.

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