Elkins Lab
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20 repositories
diff-epr
PublicDifferentiable EPR/DEER distance distribution modeling in JAXdiff-hdx
PublicDifferentiable HDX-MS prediction in JAXsynth-xtal
PublicLightweight Crystallography profile simulation from protein coordinates, with Jupyter Notebook tutorialssynth-afm
PublicDifferentiable High-Speed AFM (HS-AFM) simulation for protein structures. JAX-powered toolkit for generating synthetic movies with realistic tip-dilation and sc…diff-fret
PublicDifferentiable FRET distance distribution modeling in JAXdiff-em
PublicDifferentiable Cryo-EM map fitting in JAXdiff-ensemble
PublicDifferentiable VAE framework for predicting protein structural ensembles (IDPs) consistent with SAXS and NMR data. Built on JAX/Flax.synth-dynamics
PublicFast Langevin dynamics engine using the Anisotropic Network Model (ANM) for rapid protein conformational ensemble generation.resonance-flow
PublicJAX-native differentiable protein folding framework integrating experimental NMR constraints (RDCs) and biophysical "self-correction." Several Jupyter Notebook…diff-biophys
PublicDifferentiable biophysical modeling in JAX (SAXS, NMR, CD), with Jupyter Notebook examples.synth-cryo-em
PublicGenerate realistic synthetic 3D Cryo-EM densities from structural models for testing algorithms and training ML models.synth-nmr
PublicNMR spectroscopy calculations for protein structures. Jupyter Notebook tutorials are available to visualize the concepts.torsion-tuner
PublicGNN-based protein structure refinement using JAX-differentiable kinematics to fit solution-state experimental data (SAXS/NMR).diff-integrator
PublicIntegrative Refinement Engine for Differentiable Biophysics in JAXsynth-pdb
PublicGenerate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are availab…synth-saxs
PublicA lightweight Python library for simulating Small-Angle X-ray Scattering (SAXS) profiles from protein coordinates, with Jupyter Notebook examples.open-bcif
PublicHigh-performance, streaming-first toolkit for manipulating and validating BinaryCIF (BCIF) files at scale. Designed for structural biology.bioconda-recipes
Publicsynth-suite
Publicsynth-core
Public
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