tiwarylab/biobench-jarvis

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tiwarylab/biobench-jarvis

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Tiwary Lab contribution to the NIST JARVIS leaderboard

alphafold2rave

Jupyter Notebook

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

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RAVE

Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)

State-Predictive-Information-Bottleneck

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DDPM_REMD

Denoising diffusion probabilistic models for replica exchange

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SGOOP

Spectral Gap Optimization of Parameters

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DynamicsAE

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

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amino

Automatic Mutual Information Noise Omission

simple-diffusion

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

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kinase_Aloop

TERP

Thermodynamically Explainable Representations of AI and other black-box Paradigms

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GNN-PLUMED-Nucleation

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

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ps-LSTM

Training neural network with constraints

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SGOOP-d

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AF2RAVE_Glide-kinase

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SPIB-biophysical-applications

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

Belief-Propagation

Belief Propagation on Factor Graphs

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T4-lysozyme-loop

simulating-Langevin-dynamics

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many-angle-OP