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@Ferg-Lab Ferguson Lab at the University of Chicago

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    Repositories list

    33 repositories

    • UCG_chiral

      Public
      UCG model of a chiral molecular system
      Jupyter Notebook
      •0•0•0•0•Updated Jul 6, 2026Jul 6, 2026

    • TAR

      Public
      Takens Reconstruction package for arbitrary dynamical systems
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 11, 2026May 11, 2026

    • functionalized_cyclodextrin_pfas

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • ELP_Simulation

      Public
      Python
      •0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • ELP_Solute_Permeability

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • CAHS-Protein-Simulations

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Mar 17, 2026Mar 17, 2026

    • BayesWHAM

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 14, 2026Mar 14, 2026

    • Flow-Back

      Public
      Generative backmapping of coarse-grained molecular systems using an equivariant graph neural network and flow-matching
      Python
      •7•0•0•0•Updated Mar 2, 2026Mar 2, 2026

    • PDFT_OPESf

      Public
      Enhanced Sampling with Multi-reference Electronic Structure
      Python
      •
      MIT License
      •2•0•0•0•Updated Nov 14, 2025Nov 14, 2025

    • SiC_Allegro_MLIP

      Public
      Python
      •0•2•0•0•Updated Nov 10, 2025Nov 10, 2025

    • FEN-HTVS

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 8, 2025Sep 8, 2025

    • Cyclodextrin-PFAS_Simulations

      Public
      PFAS II cyclodextrin simulation and analysis codes
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • mof-topology-prediction

      Public
      Python
      •1•5•0•0•Updated May 28, 2025May 28, 2025

    • cmp

      Public
      Active Learning for the Design of Collagen-Mimetic Peptoids with Thermostable Triple Helical Tertiary Structures
      Jupyter Notebook
      •1•0•0•0•Updated May 17, 2025May 17, 2025

    • DiAMoNDBack

      Public
      DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces
      Python
      •5•18•2•0•Updated May 7, 2025May 7, 2025

    • principalcurve_integrin_structures

      Public
      Full-length and all-atom structures of alpha2bet3 integrin along minimum free energy pathway.
      Jupyter Notebook
      •0•2•0•0•Updated Dec 14, 2024Dec 14, 2024

    • Flow-Back-with-DNA

      Public
      Generative backmapping of coarse-grained molecular systems using an equivariant graph neural network and flow-matching
      Python
      •7•6•0•0•Updated Nov 5, 2024Nov 5, 2024

    • LSS

      Public
      Jupyter Notebook
      •2•12•0•0•Updated Oct 7, 2024Oct 7, 2024

    • LSS_BBA

      Public
      Add BBA example to LSS walkthrough
      Jupyter Notebook
      •1•0•0•0•Updated Aug 6, 2024Aug 6, 2024

    • IMSI_LSS

      Public
      IMSI hands-on workshop: Latent Space Simulators
      Jupyter Notebook
      •
      MIT License
      •3•0•0•0•Updated Apr 29, 2024Apr 29, 2024

    • snrv

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Apr 5, 2024Apr 5, 2024

    • integrin_molgen

      Public
      Deep generative modeling of large multi-molecular systems
      molecular-simulationgenerative-adversarial-networkmulti-molecular-systems
      molecular-simulationgenerative-adversarial-networkmulti-molecular-systems
      Jupyter Notebook
      •0•1•0•0•Updated Nov 26, 2023Nov 26, 2023

    • dMap_JAX

      Public
      Diffusion maps using JAX
      Python
      •
      MIT License
      •0•2•0•0•Updated Nov 7, 2023Nov 7, 2023

    • Protein_design_mmdVAE_torch

      Public
      Jupyter Notebook
      •
      MIT License
      •0•4•0•0•Updated Sep 8, 2023Sep 8, 2023

    • pines

      Public
      Permutationally invariant networks for enhanced sampling (PINES)
      molecular-simulationfree-energyenhanced-sampling
      molecular-simulationfree-energyenhanced-samplingplumedcollective-variablespermutational-invariance
      C++
      •
      MIT License
      •1•7•9•0•Updated Aug 25, 2023Aug 25, 2023

    • ChromSTEM-Denoising-Autoencoder

      Public
      A denoising autoencoder using convolutional neural networks and molecular dynamics simulations to post-process ChromSTEM images and provide nucleosome-level res…
      Jupyter Notebook
      •0•0•0•0•Updated Aug 25, 2023Aug 25, 2023

    • activeLearningPFASLinear

      Public
      Data-driven discovery of linear molecular probes with optimal selective affinity for PFAS in water
      molecular-dynamics-simulationsensorsprobes
      molecular-dynamics-simulationsensorsprobesbayesian-optimizationenhanced-samplingvariational-autoencoderpfas
      Jupyter Notebook
      •1•3•0•0•Updated Aug 22, 2023Aug 22, 2023

    • WorkCurveOptim

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Jul 17, 2023Jul 17, 2023

    • mfGPR

      Public
      Multi-fidelity Gaussian Process Regression
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•12•0•0•Updated Mar 22, 2023Mar 22, 2023

    • molgen

      Public
      Conditional Molecular Structure Generation
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•0•0•Updated Mar 3, 2023Mar 3, 2023
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