biochemistry

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

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

Scientific Computing for Chemists with Python is a free book for teaching basic coding skills to chemists using Python, Jupyter notebooks, and the other Python software. This textbook teaches a variety of Python packages including NumPy, SciPy, matplotlib, pandas, seaborn, nmrglue, SymPy, scikit-image, scikit-learn, and others.

Ribbon diagrams of proteins in #golang.

Python package to study microbial communities using metabolic modeling.

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

Computational synthetic biology: Predicting DNA edits for bioengineering

Analysis of non-covalent interactions in MD trajectories

A List of Papers on Theoretical Foundations of Graph Neural Networks

Contact map analysis for biomolecules; based on MDTraj

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

AutoML system for building trustworthy peptide bioactivity predictors

A Python parser for the BRENDA database

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

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

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

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

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

Data processing for serial crystallography

A Python package for quantum chemistry tailored toward fragment-based embedding and quantum algorithms applied to macromolecule simulations.