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brenda-database

Retrieve enzyme kinetic parameters and reaction equations from the BRENDA SOAP API.

21|2|Updated Dec 8, 2025
Search Tags:#bioinformatics#soap api#metabolic pathway#substrate specificity#kinetic modeling#enzyme kinetics#ec numbers
One-click install
npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill brenda-database-silverstein
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: brenda-database
Source: https://github.com/silverstein/claude-scientific-skills-desktop/tree/main/corpus/brenda-database
Command: npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill brenda-database-silverstein

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill helps researchers quickly find enzyme kinetic parameters and reaction information needed for biochemical characterization, metabolic pathway work, and enzyme engineering, without manually searching and reformatting results from literature.

Core Features & Use Cases

  • Kinetic parameter retrieval (Km and related fields): Look up Km values by EC number, organism, and substrate to support candidate selection and comparative analysis.
  • Reaction information (stoichiometry and equations): Fetch reaction equations associated with enzymes for interpretation, pathway mapping, and retrosynthesis support.
  • Engineering and optimization support: Identify thermophilic homologs and pH-stable variants, extract inhibition/activation cues from commentary, and assemble modeling-ready parameters for Michaelis-Menten workflows.
  • Pathway and retrosynthetic assistance: Build simple enzymatic pathways and retrosynthetic trees using available enzyme/query functions and heuristics.

Quick Start

Use the brenda-database skill to get Km and reaction data for EC number 1.1.1.1 by asking to retrieve kinetic parameters and key reactions for modeling and pathway planning.

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 from BRENDA using an EC number?▼

To retrieve enzyme kinetic parameters like Km from BRENDA, query the SOAP API using specified EC numbers, organisms, and substrates. The Skill handles authenticated SOAP calls and parses response strings to deliver structured, modeling-ready data for biochemical analysis.

What is the best way to extract reaction stoichiometry for EC-linked transformations?▼

The best way to extract reaction stoichiometry for EC-linked transformations is to fetch reaction equations directly via the BRENDA SOAP API. The Skill parses the returned data to support pathway mapping, interpretation, and retrosynthetic tree construction.

Can I use pandas and matplotlib to visualize enzyme kinetics data queried from BRENDA?▼

Yes, you can use pandas and matplotlib to visualize enzyme kinetics data queried from BRENDA. The Skill structures parsed API responses into dataframes and generates basic visualizations to support comparative substrate screening and kinetic modeling.

Do I need a BRENDA SOAP API account to fetch metabolic pathway and inhibition data?▼

Yes, you need a BRENDA SOAP API account for authentication. The Skill requires valid credentials to perform rate-limited querying, fetch metabolic pathway data, and extract inhibition or activation cues from enzyme commentary fields.

How do I screen substrate specificity and thermophilic homologs across different organisms?▼

Screen substrate specificity and thermophilic homologs across organisms by querying the BRENDA API with specific EC numbers and substrates. The Skill compares Km values and extracts pH-stable or thermophilic variants to support enzyme engineering and optimization.

Are there limitations when building retrosynthetic trees from BRENDA reaction equations?▼

Limitations exist when building retrosynthetic trees from BRENDA reaction equations because the Skill relies on available enzyme query functions and heuristics rather than complete chemical reaction databases. Rate-limited querying may also restrict large-scale pathway construction.

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