protein-design
There are 98 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
lightdock/lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
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
lucidrains/chroma-pytorch
Implementation of Chroma, generative models of protein using DDPM and GNNs, in Pytorch
samsinai/FLEXS
Fitness landscape exploration sandbox for biological sequence 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.
J-SNACKKB/FLIP
A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design
lucidrains/tr-rosetta-pytorch
Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design
RosettaCommons/rosetta
The Rosetta Bio-macromolecule modeling package.
OATML-Markslab/ProteinNPT
Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"
samuelstanton/lambo
Code to reproduce experiments in "Accelerating Bayesian Optimization for Protein Design with Denoising Autoencoders" (Stanton et al 2022)
Eikor/InstructPLM
The first large protein language model trained follows structure instructions.
lucidrains/equiformer-diffusion
Implementation of Denoising Diffusion for protein design, but using the new Equiformer (successor to SE3 Transformers) with some additional improvements
ostrokach/proteinsolver
Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.
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
wells-wood-research/timed-design
Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis
prescient-design/walk-jump
Official repository for discrete Walk-Jump Sampling (dWJS)
anton-bushuiev/PPIformer
Learning to design protein-protein interactions with enhanced generalization (ICLR24)
Shen-Lab/gcWGAN
Guided Conditional Wasserstein GAN for De Novo Protein Design
HySonLab/Protein_Redesign
Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models
XinshaoAmosWang/DeepCriticalLearning
Deep Critical Learning. Implementation of ProSelfLC, IMAE, DM, etc.
sarisabban/RosettaDesign
RosettaDesign using PyRosetta
wells-wood-research/PDBench
PDBench is a dataset and software package for evaluating fixed-backbone sequence design algorithms.
conradry/prtm
Deep learning for protein science
lightdock/lightdock-python2.7
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
google-research/slip
SLIP is a sandbox environment for engineering protein sequences with synthetic fitness functions.
HySonLab/Directed_Evolution
Protein Design by Machine Learning guided Directed Evolution
LPDI-EPFL/FunFolDesData
Rosetta FunFolDes – a general framework for the computational design of functional proteins.
NIC-SBI/CC_protein_origami
Design platform for creating single-chain polyhedral cages made from coiled-coil building modules
westlake-repl/SaprotHub
SaprotHub: Making Protein Modeling Accessible to All Biologists