Ferguson Lab at the University of Chicago

All

19 repositories

mof-topology-prediction
Public
Python
•0•0•0•0•Updated Nov 19, 2024Nov 19, 2024
Flow-Back
Public
Generative backmapping of coarse-grained molecular systems using an equivariant graph neural network and flow-matching
Python
•2•0•0•0•Updated Nov 5, 2024Nov 5, 2024
LSS
Public
Jupyter Notebook
•2•8•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
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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
DiAMoNDBack
Public
DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces
Python
•5•18•2•0•Updated Feb 29, 2024Feb 29, 2024
integrin_molgen
Public
Deep generative modeling of large multi-molecular systems
molecular-simulation generative-adversarial-network multi-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•1•0•0•Updated Nov 7, 2023Nov 7, 2023
Protein_design_mmdVAE_torch
Public
Jupyter Notebook
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MIT License
•0•4•0•0•Updated Sep 8, 2023Sep 8, 2023
pines
Public
Permutationally invariant networks for enhanced sampling (PINES)
molecular-simulation free-energy enhanced-sampling plumed collective-variables permutational-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-simulation sensors probes bayesian-optimization enhanced-sampling variational-autoencoder pfas
Jupyter Notebook
•1•2•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•8•0•0•Updated Mar 22, 2023Mar 22, 2023
molgen
Public
Conditional Molecular Structure Generation
Python
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BSD 3-Clause "New" or "Revised" License
•0•3•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
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MIT License
•0•0•0•0•Updated Nov 16, 2022Nov 16, 2022