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    29 repositories

    • af2rave

      Public
      Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Dec 17, 2024Dec 17, 2024

    • model-comparison

      Public
      Jupyter Notebook
      •0•4•0•0•Updated Nov 14, 2024Nov 14, 2024

    • TERP

      Public
      Thermodynamically Explainable Representations of AI and other black-box Paradigms
      Jupyter Notebook
      •
      MIT License
      •5•30•0•0•Updated Nov 3, 2024Nov 3, 2024

    • GrASP

      Public
      Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention
      Python
      •
      MIT License
      •5•49•6•0•Updated Oct 21, 2024Oct 21, 2024

    • amino

      Public
      Automatic Mutual Information Noise Omission
      Python
      •
      MIT License
      •2•14•2•0•Updated Oct 8, 2024Oct 8, 2024

    • alphafold2rave

      Public
      Jupyter Notebook
      •
      MIT License
      •8•63•4•0•Updated Jul 3, 2024Jul 3, 2024

    • AF2RAVE_Glide-kinase

      Public
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Jul 3, 2024Jul 3, 2024

    • SPIB_kinetics

      Public
      Jupyter Notebook
      •1•5•0•0•Updated Apr 11, 2024Apr 11, 2024

    • hydrophobic-ligand-dissociation

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 5, 2024Mar 5, 2024

    • GNN-PLUMED-Nucleation

      Public
      C++
      •
      MIT License
      •0•6•0•0•Updated Feb 1, 2024Feb 1, 2024

    • simple-diffusion

      Public
      Demo of diffusion models #DDPM applied to molecular dynamics of small peptide
      Jupyter Notebook
      •1•13•0•0•Updated Jan 26, 2024Jan 26, 2024

    • kinase_Aloop

      Public
      Python
      •1•9•0•0•Updated Oct 25, 2023Oct 25, 2023

    • SPIB-plumed-masterclass-2022

      Public
      Jupyter Notebook
      •
      MIT License
      •3•9•0•0•Updated Sep 21, 2023Sep 21, 2023

    • DynamicsAE

      Public
      A deep learning-based framework to uniquely identify an uncorrelated, isometric and meaningful latent representation.
      Jupyter Notebook
      •
      MIT License
      •1•17•0•0•Updated Sep 12, 2023Sep 12, 2023

    • biobench-jarvis

      Public
      Tiwary Lab contribution to the NIST JARVIS leaderboard
      Jupyter Notebook
      •0•1•0•0•Updated Jun 7, 2023Jun 7, 2023

    • State-Predictive-Information-Bottleneck

      Public
      Jupyter Notebook
      •
      MIT License
      •0•25•0•0•Updated May 31, 2023May 31, 2023

    • Driving-and-characterizing-nucleation-of-urea-and-glycine-polymorphs-in-water

      Public
      PLUMED Nest files for metadynamics simulations of urea and glycine nucleation in water
      MIT License
      •0•6•0•0•Updated Jan 20, 2023Jan 20, 2023

    • ps-LSTM

      Public
      Training neural network with constraints
      Jupyter Notebook
      •
      MIT License
      •2•4•2•0•Updated Jun 23, 2022Jun 23, 2022

    • LSTM-predict-MD

      Public
      Learning Molecular Dynamics with Simple Language Model built upon Long Short-Term Memory Neural Network
      Jupyter Notebook
      •
      MIT License
      •4•44•1•0•Updated Jun 23, 2022Jun 23, 2022

    • many-angle-OP

      Public
      C++
      •
      MIT License
      •0•1•0•0•Updated Mar 31, 2022Mar 31, 2022

    • jacobian

      Public
      Codes for calculating the Jacobian for a nonlinear latent space and decomposing the free-energy along the one-dimensional latent space profiles
      Jupyter Notebook
      •1•1•0•0•Updated Mar 17, 2022Mar 17, 2022

    • SPIB-biophysical-applications

      Public
      Application of SPIB to study protein conformational dynamics and membrane permeation.
      Python
      •
      MIT License
      •1•2•0•0•Updated Mar 13, 2022Mar 13, 2022

    • DDPM_REMD

      Public
      Denoising diffusion probabilistic models for replica exchange
      Jupyter Notebook
      •
      MIT License
      •4•23•0•0•Updated Feb 19, 2022Feb 19, 2022

    • SGOOP-d

      Public
      Jupyter Notebook
      •
      MIT License
      •0•3•1•0•Updated Jan 19, 2022Jan 19, 2022

    • simulating-Langevin-dynamics

      Public
      Jupyter Notebook
      •
      MIT License
      •2•1•0•0•Updated Nov 30, 2021Nov 30, 2021

    • Belief-Propagation

      Public
      Belief Propagation on Factor Graphs
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jul 7, 2021Jul 7, 2021

    • RAVE

      Public
      Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)
      Python
      •
      MIT License
      •3•42•2•0•Updated May 3, 2020May 3, 2020

    • T4-lysozyme-loop

      Public
      MIT License
      •1•1•0•0•Updated Apr 8, 2020Apr 8, 2020

    • SGOOP

      Public
      Spectral Gap Optimization of Parameters
      Jupyter Notebook
      •
      MIT License
      •7•17•2•0•Updated Mar 28, 2020Mar 28, 2020