Can this skill help with enzyme engineering?

Absolutely. It includes specialized functions to find thermophilic homologs, pH-stable variants, and analyze substrate specificity to support enzyme optimization studies.

Does it support kinetic modeling?

Yes, the skill provides tools to extract modeling-ready parameters (Km, Vmax, kcat) and can even generate Michaelis-Menten plots and other visualizations using matplotlib.

How can I search for enzymes if I don't know the EC number?

You can use the built-in search functions to find enzymes by substrate name, product name, or even specific reaction patterns like 'oxidation'.

What is the BRENDA database?

BRENDA (BRaunschweig ENzyme DAtabase) is the world's most comprehensive enzyme information system, containing millions of data points on kinetic parameters, reactions, and optimal conditions curated from scientific literature.

Do I need an account to use the brenda-database skill?

Yes, you must register for a free account at brenda-enzymes.org and set your credentials using BRENDA_EMAIL and BRENDA_PASSWORD environment variables.

BRENDA Enzyme Database Integration

Name: BRENDA Enzyme Database Integration
Author: x-cmd

byx-cmd

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データサイエンスとML

Provides comprehensive access to the BRENDA enzyme database for retrieving kinetic parameters, reaction stoichiometry, and organism-specific biochemical data.

This skill enables Claude to interact with the world's most extensive enzyme information system, BRENDA, via its SOAP API. It allows users to programmatically retrieve critical biochemical data such as Michaelis-Menten constants (Km), turnover numbers (kcat), reaction equations, and optimal environmental conditions. It is particularly valuable for metabolic pathway reconstruction, enzyme engineering, and kinetic modeling, providing researchers with the tools to compare enzyme properties across different organisms and identify optimal targets for biotechnological applications.

主な機能

019 GitHub stars

02Access detailed reaction stoichiometry and substrate-specific information

03Identify enzyme inhibitors, activators, and cofactor requirements

04Retrieve kinetic parameters like Km, kcat, and Vmax for over 45,000 enzymes

05Query optimal pH, temperature, and environmental stability data

06Search for enzymes by substrate, product, or reaction pattern

ユースケース

01Collecting standardized kinetic data for biochemical modeling and simulations

02Metabolic pathway reconstruction and retrosynthetic route planning

03In silico enzyme engineering and identifying heat-stable homologs

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add x-cmd/skill brenda-database

For use in Claude.ai and ChatGPT

Download Skill