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af2rave_glide-kinase

alphafold2rave

amino

Automatic Mutual Information Noise Omission

belief-propagation

Belief Propagation on Factor Graphs

biobench-jarvis

Tiwary Lab contribution to the NIST JARVIS leaderboard

ddpm_remd

Denoising diffusion probabilistic models for replica exchange

driving-and-characterizing-nucleation-of-urea-and-glycine-polymorphs-in-water

PLUMED Nest files for metadynamics simulations of urea and glycine nucleation in water

dynamicsae

A deep learning-based framework to uniquely identify an uncorrelated, isometric and meaningful latent representation.

gnn-plumed-nucleation

grasp

Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention

hydrophobic-ligand-dissociation

jacobian

Codes for calculating the Jacobian for a nonlinear latent space and decomposing the free-energy along the one-dimensional latent space profiles

kinase_aloop

lstm-predict-md

Learning Molecular Dynamics with Simple Language Model built upon Long Short-Term Memory Neural Network

many-angle-op

ps-lstm

Training neural network with constraints

rave

Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)

sgoop

Spectral Gap Optimization of Parameters

sgoop-d

simple-diffusion

Demo of diffusion models #DDPM applied to molecular dynamics of small peptide

simulating-langevin-dynamics

spib-biophysical-applications

Application of SPIB to study protein conformational dynamics and membrane permeation.

spib-plumed-masterclass-2022

spib_kinetics

state-predictive-information-bottleneck

t4-lysozyme-loop

terp

Thermodynamically Explainable Representations of AI and other black-box Paradigms