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Generate realistic synthetic 3D Cryo-EM densities from structural models for testing algorithms and training ML models.
Python 2
JAX-native differentiable protein folding framework integrating experimental NMR constraints (RDCs) and biophysical "self-correction." Several Jupyter Notebooks visualize the concepts.
Lightweight Crystallography profile simulation from protein coordinates, with Jupyter Notebook tutorials
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 VAE framework for predicting protein structural ensembles (IDPs) consistent with SAXS and NMR data. Built on JAX/Flax.
Fast Langevin dynamics engine using the Anisotropic Network Model (ANM) for rapid protein conformational ensemble generation.
Differentiable biophysical modeling in JAX (SAXS, NMR, CD), with Jupyter Notebook examples.
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