protein-design
There are 135 repositories under protein-design topic.
Peldom/papers_for_protein_design_using_DL
List of papers about Proteins Design using Deep Learning
a-r-j/graphein
Protein Graph Library
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
RosettaCommons/PyRosetta.notebooks
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
Graylab/DL4Proteins-notebooks
Colab Notebooks covering deep learning tools for biomolecular structure prediction and design
lightdock/lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
OATML-Markslab/ProteinGym
Official repository for the ProteinGym benchmarks
RosettaCommons/rosetta
The Rosetta Bio-macromolecule modeling package.
adaptyvbio/ProteinFlow
Versatile computational pipeline for processing protein structure data for deep learning applications.
aqlaboratory/genie
De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds
samsinai/FLEXS
Fitness landscape exploration sandbox for biological sequence design.
lucidrains/chroma-pytorch
Implementation of Chroma, generative models of protein using DDPM and GNNs, in Pytorch
LPDI-EPFL/masif-neosurf
MaSIF-neosurf: surface-based protein design for ternary complexes.
BasedLabs/NoLabs
Open source biolab
OATML-Markslab/ProteinNPT
Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"
J-SNACKKB/FLIP
A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design
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.
chao1224/ProteinDT
A Text-guided Protein Design Framework, Nat Mach Intell 2025 (https://www.nature.com/articles/s42256-025-01011-z)
THUNLP-MT/PepGLAD
Codes for our paper "Full-Atom Peptide Design with Geometric Latent Diffusion" (NeurIPS 2024)
Eikor/InstructPLM
The first large protein language model trained follows structure instructions.
lucidrains/tr-rosetta-pytorch
Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design
westlake-repl/Denovo-Pinal
Text-guided protein design
AngxiaoYue/ReQFlow
[ICML 2025] 🧬 ReQFlow: Rectified Quaternion Flow for Efficient and High-Quality Protein Backbone Generation
bytedance/PXDesignBench
A Unified Evaluation Suite for Protein Design
timkartar/DeepPBS
Geometric deep learning of protein–DNA binding specificity
samuelstanton/lambo
Code to reproduce experiments in "Accelerating Bayesian Optimization for Protein Design with Denoising Autoencoders" (Stanton et al 2022)
ostrokach/proteinsolver
Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.
WaymentSteeleLab/Dyna-1
Model for predicting micro-millisecond motions from protein sequence and/or structure
wells-wood-research/timed-design
Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis
lucidrains/equiformer-diffusion
Implementation of Denoising Diffusion for protein design, but using the new Equiformer (successor to SE3 Transformers) with some additional improvements
prescient-design/walk-jump
Official repository for discrete Walk-Jump Sampling (dWJS)
Genentech/walk-jump
Official repository for discrete Walk-Jump Sampling (dWJS)
sarisabban/RamaNet
Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure
anton-bushuiev/PPIformer
Learning to design protein-protein interactions with enhanced generalization (ICLR 2024)
HySonLab/Directed_Evolution
Protein Design by Machine Learning guided Directed Evolution
LBM-EPFL/CARBonAra
Deep learning framework for protein sequence design from a backbone scaffold that can leverage the molecular context including non-protein entities.