Biochemistry Python Packages

cobra

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

59K 560 233

micom

Python package to study microbial communities using metabolic modeling.

3K 128 23

molecularnodes

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

934 1K 120

ypkpathway

Automatic pathway assembly with the YeastPathwayKit

877 2 1

corda

Genome-scale model construction with CORDA

581 25 8

contact-map

Contact maps based on MDTraj

569 48 21

efmlrs

Extracts EFMs from result file of mplrs and decompresses EFMs from efmtool and mplrs results that have been compressed with EFMlrs

502 6 1

brendapyrser

Tools to parse the BRENDA database

447 33 10

qpcr

A python package to perform analysis of qPCR data

400 28 6

life123

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

355 6 1

easymda

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

343 4 0

biosimulators-rbapy

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

309 0 0

osmolytes

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

203 1 4

mol2scad

A script to turn molecular coordinates files into SCAD files

124 0 1

helixvis

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

123 6 1

buffer-app

A collection of python scripts for chemistry and biochemistry

105 0 1

pycontact

Analysis of non-covalent interactions in MD trajectories

71 69 13