Repositories list

• 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

• FEN-HTVS

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

• ELP_Simulation

  Public
  Python

  •0•0•0•0•Updated Jun 30, 2025Jun 30, 2025

• mof-topology-prediction

  Public
  Python

  •1•2•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•19•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•1•0•0•Updated Dec 14, 2024Dec 14, 2024

• Flow-Back

  Public
  Generative backmapping of coarse-grained molecular systems using an equivariant graph neural network and flow-matching

  Python

  •4•6•0•0•Updated Nov 5, 2024Nov 5, 2024

• LSS

  Public
  Jupyter Notebook

  •2•9•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

  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+ 3plumedcollective-variablespermutational-invariance

  C++

  •

  MIT License

  •0•6•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 resolution.

  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+ 4bayesian-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

  •1•11•0•0•Updated Mar 22, 2023Mar 22, 2023

• molgen

  Public
  Conditional Molecular Structure Generation

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•5•0•0•Updated Mar 3, 2023Mar 3, 2023

• mdn_propagator

  Public
  Mixture Density Networks (MDNs) for learning simulation propagators

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Jan 25, 2023Jan 25, 2023

• ActiveLearningCG

  Public
  Jupyter Notebook

  •1•1•0•0•Updated Nov 18, 2022Nov 18, 2022

• Limits-of-single-molecule-Takens-reconstruction-notebooks

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Nov 16, 2022Nov 16, 2022