Can I use this for metabolic pathway modeling?

Absolutely. The skill includes specific helper functions and scripts designed to extract modeling parameters and support pathway reconstruction and retrosynthesis.

What kind of enzyme data can I retrieve with this skill?

The skill provides access to kinetic parameters (Km, kcat), reaction equations, organism-specific data, optimal environmental conditions (pH, temperature), and regulatory information like inhibitors and activators.

Is it possible to search for enzymes by substrate or product?

Yes, the skill allows you to discover enzymes based on specific substrates, products, or reaction patterns, making it highly effective for enzyme discovery.

Does it support data visualization?

Yes, it includes scripts to generate Michaelis-Menten plots, pH activity profiles, and temperature stability charts using Matplotlib and Seaborn.

Does the BRENDA Database skill require an account?

Yes, you must register at the BRENDA website and configure your credentials (BRENDA_EMAIL and BRENDA_PASSWORD) as environment variables to access the SOAP API.

BRENDA Enzyme Database

Name: BRENDA Enzyme Database
Author: Sologa

bySologa

Data Science & ML

Accesses the comprehensive BRENDA enzyme database to retrieve kinetic parameters, reaction equations, and biochemical data via SOAP API.

About

The BRENDA Database skill enables researchers and developers to programmatically query the world's most extensive enzyme information system. It provides a specialized interface for extracting critical biochemical data, including kinetic parameters like Km and kcat, reaction stoichiometries, and organism-specific enzyme properties. This skill is essential for professionals working in metabolic engineering, synthetic biology, and biochemical research who need to automate data collection for pathway reconstruction, enzyme optimization, and comparative genomics directly within their development workflow.

Key Features

0 GitHub stars
Retrieval of kinetic parameters including Km, kcat, and Vmax values
Multi-organism enzyme property comparison and analysis
Comprehensive database of enzyme inhibitors, activators, and cofactors
Detailed reaction equation and stoichiometry mapping for metabolic modeling
Environmental parameter tracking for optimal pH and temperature conditions

Use Cases

Identifying and comparing thermostable enzyme variants for industrial biocatalysis
Reconstructing metabolic pathways and performing flux balance analysis
Conducting retrosynthesis studies to discover novel enzymatic routes for chemical production

About

Key Features

0 GitHub stars
Retrieval of kinetic parameters including Km, kcat, and Vmax values
Multi-organism enzyme property comparison and analysis
Comprehensive database of enzyme inhibitors, activators, and cofactors
Detailed reaction equation and stoichiometry mapping for metabolic modeling
Environmental parameter tracking for optimal pH and temperature conditions

Use Cases

Identifying and comparing thermostable enzyme variants for industrial biocatalysis
Reconstructing metabolic pathways and performing flux balance analysis
Conducting retrosynthesis studies to discover novel enzymatic routes for chemical production