protein-design

There are 120 repositories under protein-design topic.

  • Peldom/papers_for_protein_design_using_DL

    List of papers about Proteins Design using Deep Learning

    1.6k1232191
  • graphein

    a-r-j/graphein

    Protein Graph Library

    Language:Jupyter Notebook1.1k17158133

  • PaddlePaddle/PaddleHelix

    Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

    Language:Python1.1k25126229

  • RosettaCommons/PyRosetta.notebooks

    Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

    Language:Jupyter Notebook55232935159

  • Graylab/DL4Proteins-notebooks

    Colab Notebooks covering deep learning tools for biomolecular structure prediction and design

    Language:Jupyter Notebook3556551
  • lightdock

    lightdock/lightdock

    Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

    Language:Python328127245

  • OATML-Markslab/ProteinGym

    Official repository for the ProteinGym benchmarks

    Language:HTML29055535

  • adaptyvbio/ProteinFlow

    Versatile computational pipeline for processing protein structure data for deep learning applications.

    Language:Python25371717

  • RosettaCommons/rosetta

    The Rosetta Bio-macromolecule modeling package.

    Language:C++2431993480

  • aqlaboratory/genie

    De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds

    Language:Python1785419
  • FLEXS

    samsinai/FLEXS

    Fitness landscape exploration sandbox for biological sequence design.

    Language:Jupyter Notebook1608722

  • lucidrains/chroma-pytorch

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

    Language:Python15818323

  • BasedLabs/NoLabs

    Open source biolab

    Language:JavaScript125499

  • LPDI-EPFL/masif-neosurf

    MaSIF-neosurf: surface-based protein design for ternary complexes.

    Language:Python1065615

  • OATML-Markslab/ProteinNPT

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

    Language:Python10602310

  • westlake-repl/SaprotHub

    Making Protein Modeling Accessible to All Biologists

    Language:Jupyter Notebook10341211

  • J-SNACKKB/FLIP

    A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

    Language:Jupyter Notebook9771115

  • lightonai/RITA

    RITA is a family of autoregressive protein models, developed by LightOn in collaboration with the OATML group at Oxford and the Debora Marks Lab at Harvard.

    Language:Python966108

  • lucidrains/tr-rosetta-pytorch

    Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design

    Language:Python794310

  • Eikor/InstructPLM

    The first large protein language model trained follows structure instructions.

    Language:Python76245

  • samuelstanton/lambo

    Code to reproduce experiments in "Accelerating Bayesian Optimization for Protein Design with Denoising Autoencoders" (Stanton et al 2022)

    Language:Jupyter Notebook6831123

  • AngxiaoYue/ReQFlow

    🧬 ReQFlow: Rectified Quaternion Flow for Efficient and High-Quality Protein Backbone Generation

    Language:Python67315

  • chao1224/ProteinDT

    A Text-guided Protein Design Framework, Nat Mach Intell 2025 (https://www.nature.com/articles/s42256-025-01011-z)

    Language:Python65535
  • DeepPBS

    timkartar/DeepPBS

    Geometric deep learning of protein–DNA binding specificity

    Language:Python644175
  • proteinsolver

    ostrokach/proteinsolver

    Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.

    Language:Jupyter Notebook59138

  • lucidrains/equiformer-diffusion

    Implementation of Denoising Diffusion for protein design, but using the new Equiformer (successor to SE3 Transformers) with some additional improvements

    561204

  • wells-wood-research/timed-design

    Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis

    Language:Python5644611

  • THUNLP-MT/PepGLAD

    Codes for our paper "Full-Atom Peptide Design with Geometric Latent Diffusion" (NeurIPS 2024)

    Language:Python53462

  • Genentech/walk-jump

    Official repository for discrete Walk-Jump Sampling (dWJS)

    Language:Python52618

  • prescient-design/walk-jump

    Official repository for discrete Walk-Jump Sampling (dWJS)

    Language:JavaScript50548

  • sarisabban/RamaNet

    Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure

    Language:Python503110

  • anton-bushuiev/PPIformer

    Learning to design protein-protein interactions with enhanced generalization (ICLR 2024)

    Language:Jupyter Notebook46574

  • HySonLab/Protein_Redesign

    ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models

    Language:Python40336

  • LBM-EPFL/CARBonAra

    Deep learning framework for protein sequence design from a backbone scaffold that can leverage the molecular context including non-protein entities.

    Language:Jupyter Notebook38107

  • EDAPINENUT/GeoAB

    This is the official repository of paper - GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation (ICML2024)

    Language:Python372710

  • Shen-Lab/gcWGAN

    Guided Conditional Wasserstein GAN for De Novo Protein Design

    Language:Roff37827