protein-design

There are 14 repositories under protein-design topic.

Peldom / papers_for_protein_design_using_DL
List of papers about Proteins Design using Deep Learning
deep-learning protein-design
1100
graphein
a-r-j / graphein
Protein Graph Library
protein protein-structure deep-learning pytorch graph-neural-networks dgl computational-biology bioinformatics structural-biology protein-data-bank protein-design geometric-deep-learning pytorch-geometric python interactomics interactome rna ppi-networks gene-regulatory-networks drug-discovery
Language:Jupyter Notebook 977
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
biocomputing machine-learning deeplearning rna-structure-prediction dti representation-learning graph-networks protein-structure-prediction self-supervised-learning ppi molecule-design protein-folding ddi protein-docking protein-design
Language:Python 787
RosettaCommons / PyRosetta.notebooks
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
pyrosetta google-colab jupyter-notebook protein-design protein-structure-prediction protein-folding protein-docking dna rna-structure-prediction rosetta
Language:Jupyter Notebook 422
lightdock
lightdock / lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
protein protein-structure protein-protein-interaction protein-docking swarm-intelligence glowworm-swarm-optimization protein-dna-interactions peptides dna docking artificial-intelligence protein-design proteomics structural-biology structural-bioinformatics bioinformatics bioinformatics-tool chemistry molecular-biology molecular-structures
Language:Python 272
adaptyvbio / ProteinFlow
Versatile computational pipeline for processing protein structure data for deep learning applications.
bioinformatics deep-learning protein-data-bank protein-design protein-structure dataset
Language:Python 168
lucidrains / chroma-pytorch
Implementation of Chroma, generative models of protein using DDPM and GNNs, in Pytorch
artificial-intelligence deep-learning denoising-diffusion graph-neural-networks protein-design
Language:Python 158
aqlaboratory / genie
De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds
diffusion-models protein-design
Language:Python 147
FLEXS
samsinai / FLEXS
Fitness landscape exploration sandbox for biological sequence design.
machine-learning benchmarking protein-design deep-learning deep-reinforcement-learning computational-biology bayesian-optimization
Language:Jupyter Notebook 139
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.
deep-learning generative-models protein-design
Language:Python 87
J-SNACKKB / FLIP
A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design
protein protein-sequences protein-design representation-learning protein-fitness-prediction protein-function-prediction
Language:Jupyter Notebook 83
lucidrains / tr-rosetta-pytorch
Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design
artificial-intelligence deep-learning protein-folding protein-design
Language:Python 78
samuelstanton / lambo
Code to reproduce experiments in "Accelerating Bayesian Optimization for Protein Design with Denoising Autoencoders" (Stanton et al 2022)
bayesian-optimization protein-design
Language:Jupyter Notebook 60
lucidrains / equiformer-diffusion
Implementation of Denoising Diffusion for protein design, but using the new Equiformer (successor to SE3 Transformers) with some additional improvements
artificial-intelligence attention-mechanisms deep-learning denoising-diffusion equivariant-networks protein-design
55
OATML-Markslab / ProteinNPT
Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"
protein-design
Language:Python 52
proteinsolver
ostrokach / proteinsolver
Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.
bioinformatics graph-neural-networks protein protein-design protein-sequence protein-structure structural-biology
Language:Jupyter Notebook 50
sarisabban / RamaNet
Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure
protein-structure machine-learning pdb dataset neural-network denovo-design denovo protein-design rmsd topology hpc ab-initio amino-acids
Language:Python 46
Genentech / walk-jump
Official repository for discrete Walk-Jump Sampling (dWJS)
antibody machine-learning protein-design protein-sequences proteins
Language:Python 43
wells-wood-research / timed-design
Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis
protein protein-design
Language:Python 42
Shen-Lab / gcWGAN
Guided Conditional Wasserstein GAN for De Novo Protein Design
generative-adversarial-networks generative-model protein protein-design protein-sequence protein-structure
Language:Roff 36
XinshaoAmosWang / DeepCriticalLearning
Deep Critical Learning. Implementation of ProSelfLC, IMAE, DM, etc.
bert-transformer convolutional-neural-networks deep-learning image-classification protein-function-prediction pytorch protein-transformer protein-classification protein-design protein-localization
Language:Python 31
sarisabban / RosettaDesign
RosettaDesign using PyRosetta
ab-initio pyrosetta pdb backbone protein-design
Language:Python 27
anton-bushuiev / PPIformer
Learning to design protein-protein interactions with enhanced generalization (ICLR24)
equivariant-representations machine-learning protein-design protein-protein-interactions proteins
Language:Jupyter Notebook 26
wells-wood-research / PDBench
PDBench is a dataset and software package for evaluating fixed-backbone sequence design algorithms.
deep-learning protein-design protein-structure proteins
Language:Python 26
lightdock-python2.7
lightdock / lightdock-python2.7
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
gso pdb swarm-intelligence scientific-computing protein-protein-docking protein-protein protein-protein-interaction protein-structure swarm protein docking simulation dna peptides anm proteins protein-design bioinformatics protein-docking-framework
Language:C++ 25
google-research / slip
SLIP is a sandbox environment for engineering protein sequences with synthetic fitness functions.
computational-biology machine-learning protein-design
Language:Python 19
LPDI-EPFL / FunFolDesData
Rosetta FunFolDes – a general framework for the computational design of functional proteins.
protein-design rosetta publication-data functional-protein-design protein-structure protein-protein-interaction structural-biology
Language:Scala 18
NIC-SBI / CC_protein_origami
Design platform for creating single-chain polyhedral cages made from coiled-coil building modules
3d-models protein-origami python protein-design coiled-coil
Language:Python 18
HySonLab / Directed_Evolution
Protein Design by Machine Learning guided Directed Evolution
directed-evolution large-language-models protein-design proteins
Language:Python 17
microsoft / protein-uq
Benchmarking uncertainty quantification methods on proteins.
active-learning protein protein-design protein-fitness-prediction protein-function-prediction protein-sequences uncertainty-estimation uncertainty-neural-networks uncertainty-quantification
Language:Shell 17
conradry / prtm
Deep learning for protein science
deep-learning protein-science protein-design protein-folding drug-discovery
Language:Python 16
dtischer / trdesign-motif
Codebase for our preprint using trRosetta to design proteins with discontinuous functional sites, found here: https://www.biorxiv.org/content/10.1101/2020.11.29.402743v1.abstract
protein-design deep-learning
Language:Python 16
wells-wood-research / de-stress
DE-STRESS is a model evaluation pipeline that aims to make protein design more reliable and accessible.
bioinformatics pipeline protein protein-design protein-structure structural-biology webapp
Language:Elm 15
LPDI-EPFL / rstoolbox
Python Toolbox For Rosetta Silent Files Processing
science protein-design protein-sequence data-visualization data-analysis
Language:Python 14
psalveso / pyRIF
Using Rotamer Interaction Fields from RIFGen/Dock in python
pyrosetta rosetta protein-design rifdock
Language:Python 12
sarisabban / Pose
A bare metal Python library for building and manipulating protein molecular structures
amino-acids bioinformatics computational-biology denovo denovo-design pdb pose protein-design protein-structure topology biomolecular-simulation biomolecule molecular-simulation molecule protein proteins game-engine numpy python
Language:Python 11

protein-design

Peldom / papers_for_protein_design_using_DL

a-r-j / graphein

PaddlePaddle / PaddleHelix

RosettaCommons / PyRosetta.notebooks

lightdock / lightdock

adaptyvbio / ProteinFlow

lucidrains / chroma-pytorch

aqlaboratory / genie

samsinai / FLEXS

lightonai / RITA

J-SNACKKB / FLIP

lucidrains / tr-rosetta-pytorch

samuelstanton / lambo

lucidrains / equiformer-diffusion

OATML-Markslab / ProteinNPT

ostrokach / proteinsolver

sarisabban / RamaNet

Genentech / walk-jump

wells-wood-research / timed-design

Shen-Lab / gcWGAN

XinshaoAmosWang / DeepCriticalLearning

sarisabban / RosettaDesign

anton-bushuiev / PPIformer

wells-wood-research / PDBench

lightdock / lightdock-python2.7

google-research / slip

LPDI-EPFL / FunFolDesData

NIC-SBI / CC_protein_origami

HySonLab / Directed_Evolution

microsoft / protein-uq

conradry / prtm

dtischer / trdesign-motif

wells-wood-research / de-stress

LPDI-EPFL / rstoolbox

psalveso / pyRIF

sarisabban / Pose