Public notebooks hosted on Binder, Colab or Huggingface

A course with multiple chapters for beginners in protein ML. Covers Discriminative models, generative models, language models and structure based models.

proteinsmachine learningprotein design

IDPGan

IdpGAN is a GAN trained to generate ensembles of 3D conformations of coarse grained (CG) protein molecules

proteinsmdcoarse graining

AF Relax design

Efficient and scalable de novo protein design using a relaxed sequence space

proteinsprotein design

340

CHARMM-GUI+OpenMM

Using inputs from CHARMM-GUI solution builder and MD simulations with OpenMM

proteinsBiomd

281

Molecular Transformer for Reaction Prediction

A short tutorial on how to train a Molecular Transformer model (https://pubs.acs.org/doi/full/10.1021/acscentsci.9b00576) on the USPTO_MIT dataset.

machine learningchemoinformatics

Metal3D

Zinc site prediction with a single structure as input

proteinsligandsmetal

DiffLinker: Equivariant Molecular Linker Design

Equivariant 3D-Conditional Diffusion Model for Molecular Linker Design

Geometric deep learning

169

Smilesdrawer Gradio

How to use SMILES viewer on Gradio

chemoinformatics

AlphaFold2-RAVE on 1HZB cold shock proein

AlphaFold2-RAVE is an efficient protocol using the structural outputs from AlphaFold2 as initializations for AI augmented molecular dynamics. These simulations result in Boltzmann ranked ensembles.

mdmachine learningalphafold