Tiwary Lab - Artificial Chemical Intelligence

alphafold2rave

GrASP

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

LSTM-predict-MD

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

RAVE

Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)

State-Predictive-Information-Bottleneck

DDPM_REMD

Denoising diffusion probabilistic models for replica exchange

DynamicsAE

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

SGOOP

Spectral Gap Optimization of Parameters

amino

Automatic Mutual Information Noise Omission

simple-diffusion

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

kinase_Aloop

GNN-PLUMED-Nucleation

TERP

Thermodynamically Explainable Representations of AI and other black-box Paradigms

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

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

SPIB_kinetics

SPIB-plumed-masterclass-2022

ps-LSTM

Training neural network with constraints

SGOOP-d

Belief-Propagation

Belief Propagation on Factor Graphs

biobench-jarvis

Tiwary Lab contribution to the NIST JARVIS leaderboard

many-angle-OP

simulating-Langevin-dynamics

SPIB-biophysical-applications

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

T4-lysozyme-loop

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