Biochemistry Python Packages

cobra

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

brendapyrser

A Python parser for the BRENDA database

molecularnodes

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

micom

Python package to study microbial communities using metabolic modeling.

probixi

Self-Calibrating Probabilistic Peak Detection for Serial X-Ray Crystallography

ypkpathway

Automatic pathway assembly with the YeastPathwayKit

efmlrs

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

qpcr

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

life123

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

contact-map

Contact map analysis for biomolecules; based on MDTraj

corda

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

easymda

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

biosimulators-rbapy

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

osmolytes

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

helixvis

Visualize alpha-helical peptide sequences in Python using helical wheels and wenxiang diagrams

pathway-auditor

Framework for creating and validating biochemical pathway benchmarks

pycontact

Analysis of non-covalent interactions in MD trajectories

mol2scad

A collection of python scripts for chemistry and biochemistry

buffer-app

A collection of python scripts for chemistry and biochemistry