Biochemistry Python Packages

cobra

COBRApy is a package for constraint-based modeling of metabolic networks.

micom

Python package to study microbial communities using metabolic modeling.

molecularnodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

contact-map

Contact maps based on MDTraj

ypkpathway

Automatic pathway assembly with the YeastPathwayKit

efmlrs

Python package and workflow for EFM calculation via (mp)lrs and efmtool

life123

Dynamical modeling of biological systems in 1, 2 and 3D - incl. diffusion, reactions & compartments. A platform for quantitative reactomics (Python, JupyterLab, Plotly)

corda

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

qpcr

A python package to analyse qPCR data for single-use or high-throughput application

pathway-auditor

Python framework for validating biochemical pathways

biosimulators-rbapy

RBApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

easymda

Python package for easy analysis of MD simulations based on MDAnalysis.

brendapyrser

A Python parser for the BRENDA database

osmolytes

This code attempts to predict the influence of osmolytes on protein stability

helixvis

Create 2-dimensional visualizations of alpha-helical peptide sequences

mol2scad

A collection of python scripts for chemistry and biochemistry

buffer-app

A quick GUI to quickly calculate buffer dilution and adjustment.

pycontact

PyContact