ykiiiiii

gemma_pytorch

The official PyTorch implementation of Google's Gemma models

ColabFold

Making Protein folding accessible to all!

schedule_free

Schedule-Free Optimization in PyTorch

esm

conditional-flow-matching

TorchCFM: a Conditional Flow Matching library

OpenCRISPR

AI-generated gene editing systems

evo

Biological foundation modeling from molecular to genome scale

alphafold3-pytorch

Implementation of Alphafold 3 in Pytorch

RoseTTAFold-All-Atom

geometric-gnn-dojo

Geometric GNN Dojo provides unified implementations and experiments to explore the design space of Geometric Graph Neural Networks.

Score-Entropy-Discrete-Diffusion

[ICML 2024 Best Paper] Discrete Diffusion Modeling by Estimating the Ratios of the Data Distribution (https://arxiv.org/abs/2310.16834)

p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

DeepH-pack

Deep neural networks for density functional theory Hamiltonian.

LigandMPNN

mol_opt

protpardelle

Diffusion-based all-atom protein generative model.

geometric-rna-design

gRNAde: Geometric Deep Learning for 3D RNA inverse design

multiflow

ProteinNPT

Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"

DGraphDTA

a novel DTA predition method using graph neural network

protein-dpo

Aligning protein generative models with experimental fitness

rnaflow

RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching

tauLDR

Code for the paper https://arxiv.org/abs/2205.14987v2

discrete-langevin

alphafold3-pytorch-lightning-hydra

Implementation of AlphaFold 3 in PyTorch Lightning + Hydra

LatentDE

Latent-based Directed Evolution guided by Gradient Ascent for Protein Design

holo-bench

Benchmark for Biophysical Sequence Optimization Algorithms

Awesome-List-Protein-Binding-Site-Prediction-

List of papers on protein binding site prediction

delensalot

Curved-sky iterative CMB lensing tools

Bayesian_L_half

MCMC and Optimization algorithm for L_half prior