tianyu-lu

cheap-proteins

Joint embedding of protein sequence and structure with discrete and continuous compressions of protein folding model latent spaces. https://www.biorxiv.org/content/10.1101/2024.08.06.606920v1

mdgen

Generative modeling of molecular dynamics trajectories

OmegaFold

OmegaFold Release Code

alphafold3-pytorch

Implementation of Alphafold 3 in Pytorch

esm

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

edm2

Analyzing and Improving the Training Dynamics of Diffusion Models (EDM2)

LigandMPNN

model-angelo

Automatic atomic model building program for cryo-EM maps

RoseTTAFold-All-Atom

pyX-Struct

Python tool for scraping geometric X-ray Data from the Cambridge Structural Database

multiflow

ProteinWorkshop

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

alphaflow

AlphaFold Meets Flow Matching for Generating Protein Ensembles

chroma

A generative model for programmable protein design

pytorch_memlab

Profiling and inspecting memory in pytorch

FAIR

NeurIPS 2023 Spotlight paper: Full atom protein pocket design via iterative refinement

ScoreDiffusionModel

The Pytorch Tutorial of Score-based and Diffusion Model

zotero-night

Night theme for Zotero UI and PDF

RFdiffusion

Code for running RFdiffusion

chroma-pytorch

Implementation of Chroma, generative models of protein using DDPM and GNNs, in Pytorch

redshift

Redshift adjusts the color temperature of your screen according to your surroundings. This may help your eyes hurt less if you are working in front of the screen at night.

TARGET-VAE

Source code for "Unsupervised Object Representation Learning using Translation and Rotation Group Equivariant VAE," in pytorch. NeurIPS 2022

LiGAN

Deep generative models of 3D grids for structure-based drug discovery

alphafold_finetune

Python code for fine-tuning AlphaFold to perform protein-peptide binding predictions

gvp-pytorch

Geometric Vector Perceptrons --- a rotation-equivariant GNN for learning from biomolecular structure

AutoRotLib

e3_diffusion_for_molecules

lm-gvp

LM-GVP: A Generalizable Deep Learning Framework for Protein Property Prediction from Sequence and Structure

ColabDesign

Making Protein Design accessible to all via Google Colab!