Differentiable HDX-MS prediction in JAX

Differentiable FRET distance distribution modeling in JAX

Differentiable EPR/DEER distance distribution modeling in JAX

Differentiable Cryo-EM map fitting in JAX

Differentiable High-Speed AFM (HS-AFM) simulation for protein structures. JAX-powered toolkit for generating synthetic movies with realistic tip-dilation and scanning lag.

Differentiable biophysical modeling in JAX (SAXS, NMR, CD), with Jupyter Notebook examples.

Fast Langevin dynamics engine using the Anisotropic Network Model (ANM) for rapid protein conformational ensemble generation.

A lightweight Python library for simulating Small-Angle X-ray Scattering (SAXS) profiles from protein coordinates, with Jupyter Notebook examples.

JAX-native differentiable protein folding framework integrating experimental NMR constraints (RDCs) and biophysical "self-correction." Several Jupyter Notebooks visualize the concepts.

Differentiable VAE framework for predicting protein structural ensembles (IDPs) consistent with SAXS and NMR data. Built on JAX/Flax.

GNN-based protein structure refinement using JAX-differentiable kinematics to fit solution-state experimental data (SAXS/NMR).

Build conformational representations of Intrinsically Disordered Proteins and Regions by a guided sampling of the protein torsion space

Structural Python (Back) Calculator Interface for PDBs

High-performance, streaming-first toolkit for manipulating and validating BinaryCIF (BCIF) files at scale. Designed for structural biology.

Generate realistic synthetic 3D Cryo-EM densities from structural models for testing algorithms and training ML models.

Warp is an agentic development environment, born out of the terminal.

This repo is based on clauswilke/PeptideBuilder and Lun4m/PeptideBuilder.

Code for running RFdiffusion

our in-house version of ProteinMPNN

NMR spectroscopy calculations for protein structures. Jupyter Notebook tutorials are available to visualize the concepts.

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

AlphaFold 3 inference pipeline.

Open standard for machine learning interoperability

Learning to Program via Python, and Scientific Python for Programmers course material

A Python API for the RCSB Protein Data Bank (PDB)

Computational Physics for Undergraduates with Python

Open source code for AlphaFold 2.