biochemistry

opencobra/cobrapy

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

fogleman/ribbon

Ribbon diagrams of proteins in #golang.

weisscharlesj/SciCompforChemists

Scientific Computing for Chemists is a free text for teaching basic computing skills to chemists using Python, Jupyter notebooks, and the other Python packages. This text makes use of a variety of packages including NumPy, SciPy, matplotlib, pandas, seaborn, nmrglue, SymPy, scikit-image, and scikit-learn.

copasi/COPASI

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.

micom-dev/micom

Python package to study microbial communities using metabolic modeling.

20n/act

Computational synthetic biology: Predicting DNA edits for bioengineering

maxscheurer/pycontact

Analysis of non-covalent interactions in MD trajectories

katrinleinweber/PhD-thesis

Experimental tech-demo for PhD thesis in Scientific Markdown; official:

dwhswenson/contact_map

Contact map analysis for biomolecules; based on MDTraj

jaleezyy/covid-19-signal

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

jiaqingxie/Theories-of-Graph-Neural-Networks

A List of Papers on Theoretical Foundations of Graph Neural Networks

Robaina/BRENDApyrser

A Python parser for the BRENDA database

resendislab/corda

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

NoahHenrikKleinschmidt/qpcr

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

IBM/AutoPeptideML

AutoML system for building trustworthy peptide bioactivity predictors

m2d2-labs/awesome-ml-for-biochemistry

Community-curated resources for research at the intersection of AI and molecular sciences

ddoak/peppy

A VR app which allows creation and manipulation of dynamic models of polypeptides. Focus is fun and learning.

HussainAther/biology

genomics, biochemistry, biotechnology, cell biology, biophysics, ecology

shyambhakta/wetlabcalc

Wetlab Calculator

taw10/crystfel

Data processing for serial crystallography

avaamini/protease_activity_analysis

Python toolkit and package for analyzing enzyme activity data

shiwentao00/Graphsite-classifier

Ligand-binding site classification with deep graph neural networks.

gitter-lab/pria_lifechem

Virtual screening on PriA-SSB and RMI-FANCM with the LifeChem library

PPDimitrakova20/Sol-Invictus

A game where a roomba discovers amino-acids

weisscharlesj/BiopythonRamachandran

AvocadosConstant/vax

🦠 Understanding the BioNTech SARS-CoV-2 mRNA vaccine genome.

gitter-lab/pria-ams-enamine

Virtual screening on PriA-SSB with the AMS and Enamine REAL libraries

alvinwan/storm

semi-supervised deep learning for classification of molecular structures

Chlanda-Lab/cryoCLEM

Toolbox for post-correlation cryo-CLEM workflow developed at Chlanda Lab, Heidelberg University.

hrshainik/biofidelicx-diary

biofidelicX diary is the ideal location to stay informed and up-to-date on the most recent research and discoveries in bio-science, whether you're a student, a scientist, or simply someone with a passion for learning about the natural world.

NilavoBoral/Therapeutics-Data-Commons

Single-instance Prediction of small-molecule drug.

subramv/helixvis

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

BeeAnka/EFMlrs

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

justinrporter/exposons-with-jug

Use the parallelization framework jug to build exposons!

samberry19/evcomplex-interaction-scoring

Code for using EVcomplex to generate "interaction scores" for individual sequences in a multiple sequence alignment.