Modelling Enzyme Kinetics with COPASI

COPASI

• In terms of functionality, COPASI software is the best software for modelling steady-state and kinetic enzyme data. The software has the capability to do a wide range of fitting. We will be using it with Python.

Available Python Modules

• Python Bindings for Python
• Python-Copasi
• Basico
  • Prerequisite Modules: Python-Copasi, Pandas
  • Documentation
• PyCoTools
• SMBL
• MASSpy
• rxnlvl - plotting reaction levels
• rdkit - plotting enzymatic reactions (chemoinformatics toolkit)
• ELDAD- Python module for energy level diagrams.
• chempy- ChemPy is a Python package useful for solving problems in chemistry.

Basico

1. !pip install basico
   1. Maybe a different basico out there in the Python-verse
   2. Therefore, I uninstalled !pip uninstall basico
   3. Install git
      1. conda install -c anaconda git
2. !pip install git+https://github.com/copasi/basico.git

• Breakdown of Basico