Can I search for enzymes without knowing the EC number?

Yes, the skill provides functions to search for enzymes by substrate name, product name, or specific reaction patterns, making it ideal for enzyme discovery.

Can I use this for metabolic pathway design?

Absolutely. The skill includes an enzyme pathway builder that helps find enzymatic steps and build retrosynthetic trees for target molecules.

How do I authenticate with the BRENDA database using this skill?

You must register for an account at the official BRENDA website and then set your credentials as BRENDA_EMAIL and BRENDA_PASSWORD in your environment variables or a .env file.

Does this skill support data visualization?

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

What kind of kinetic data can I retrieve?

You can retrieve Km values, kcat (turnover numbers), Vmax, Ki (inhibition constants), and IC50 values, often filterable by specific organisms and substrates.

BRENDA Enzyme Database

Name: BRENDA Enzyme Database
Author: K-Dense-AI

byK-Dense-AI

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3,719

Data Science & ML

Accesses the comprehensive BRENDA enzyme database to retrieve kinetic parameters, biochemical reactions, and metabolic pathway data.

About

This skill integrates Claude with the BRENDA (Braunschweig Enzyme Database) SOAP API, allowing researchers and bioinformaticians to programmatically access millions of enzyme data points. It provides specialized functions for querying kinetic constants like Km and kcat, searching reactions by EC number or substrate, and analyzing environmental factors such as optimal pH and temperature across diverse organisms. Whether you are performing metabolic engineering, reconstructing biological pathways, or designing enzyme variants, this skill streamlines the process of extracting, parsing, and visualizing critical biochemical information directly within your coding environment.

Key Features

Retrieve detailed reaction equations, stoichiometry, and cofactor requirements by EC number.
Query kinetic parameters including Km, kcat, and Vmax values for millions of entries.
Generate visualizations for Michaelis-Menten kinetics and pH/temperature profiles.
Search for enzymes based on specific substrates, products, or reaction patterns.
Compare enzyme properties and environmental stabilities across multiple organisms.
3,719 GitHub stars

Use Cases

Enzyme engineering projects identifying thermophilic or pH-stable homologs for industrial use.
Kinetic modeling of biochemical systems for systems biology research and simulation.
Metabolic pathway reconstruction and retrosynthesis analysis for synthetic biology.

About

Key Features

Retrieve detailed reaction equations, stoichiometry, and cofactor requirements by EC number.
Query kinetic parameters including Km, kcat, and Vmax values for millions of entries.
Generate visualizations for Michaelis-Menten kinetics and pH/temperature profiles.
Search for enzymes based on specific substrates, products, or reaction patterns.
Compare enzyme properties and environmental stabilities across multiple organisms.
3,719 GitHub stars

Use Cases

Enzyme engineering projects identifying thermophilic or pH-stable homologs for industrial use.
Kinetic modeling of biochemical systems for systems biology research and simulation.
Metabolic pathway reconstruction and retrosynthesis analysis for synthetic biology.