Oxer11

ProSST

Code for ProSST: A Pre-trained Protein Sequence and Structure Transformer with Disentangled Attention.

score_sde

Official code for Score-Based Generative Modeling through Stochastic Differential Equations (ICLR 2021, Oral)

edm

Elucidating the Design Space of Diffusion-Based Generative Models (EDM)

alphaflow

AlphaFold Meets Flow Matching for Generating Protein Ensembles

SaProt

Saprot: Protein Language Model with Structural Alphabet

holoprot

Multi-Scale Representation Learning on Proteins (NeurIPS 2021)

robust-laplacians-py

Build high-quality Laplace matrices on meshes and point clouds in Python. Implements [Sharp & Crane SGP 2020].

equiformer_v2

[ICLR'24] EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations

DiffDock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

DynamicBind

repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

esm-s

Structure-Informed Protein Language Model

discrete_flow_models

Code for the paper https://arxiv.org/abs/2402.04997

I2SB

Str2Str

Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)

scalar-fields

Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms

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)

ProteinNPT

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

DSMBind

protein-vec

Repository for Protein-Vec, a protein embedding mixture of experts model

chroma

A generative model for programmable protein design

Tranception

Official repository for the paper "Tranception: Protein Fitness Prediction with Autoregressive Transformers and Inference-time Retrieval"

DDBM

ULTRA

A foundation model for knowledge graph reasoning

ESM-GearNet

ESM-GearNet for Protein Structure Representation Learning (https://arxiv.org/abs/2303.06275)

ProMEP

Zero-shot prediction of mutation effects on protein function with multimodal deep representation learning

conditional-flow-matching

TorchCFM: a Conditional Flow Matching library

deepblast

Neural Networks for Protein Sequence Alignment

Structure-informed_PLM

Protein language modeling with information from structures

DiffPack

Implementation of DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing

GeoDock

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.