protein-structure-prediction

There are 17 repositories under protein-structure-prediction topic.

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 ddi deeplearning dti graph-networks machine-learning molecule-design ppi protein-design protein-docking protein-folding protein-structure-prediction representation-learning rna-structure-prediction self-supervised-learning
Language:Python 795
lucidrains / alphafold3-pytorch
Implementation of Alphafold 3 in Pytorch
artificial-intelligence attention-mechanisms deep-learning denoising-diffusion protein-structure-prediction transformers
Language:Python 470
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 436
Urinx / alphafold_pytorch
An implementation of the DeepMind's AlphaFold based on PyTorch for research
alphafold protein-structure-prediction contact-prediction deep-learning pytorch-implementation casp13 structure-prediction
Language:Python 384
aqlaboratory / rgn
Recurrent Geometric Networks for end-to-end differentiable learning of protein structure
protein-structure protein-structure-prediction deep-learning deep-neural-networks
Language:Python 326
af2complex
FreshAirTonight / af2complex
Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
bioinformatics deep-learning alphafold2 protein-complexes protein-protein-interaction protein-structure-prediction protein-protein-docking
Language:Python 138
zjunlp / OntoProtein
[ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding
protein-protein-interaction gene-ontology protein-pretraining protein-function-prediction protein-structure-prediction knowledge-graph protein ontoprotein bert nlp pytorch pretrained-models pretraining iclr iclr2022
Language:Python 135
twoXes / awesome-structural-bioinformatics
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
molecular-informatics chemistry machine-learning deep-learning cheminformatics biology quantum-chemistry docking protein alphafold protein-structure-prediction awesome-list bioinformatics bioinformatics-pipeline bioinformatics-analysis proteomics genomics genetics genome-alignment protein-structure
Language:Python 56
psipred / DMPfold
De novo protein structure prediction using iteratively predicted structural constraints
deep-learning protein-sequence protein-structure protein-structure-prediction resnet
Language:C 55
psipred / DMPfold2
Fast and accurate protein structure prediction
protein-structure-prediction deep-learning multiple-sequence-alignment end-to-end
Language:Python 46
mircare / Porter5
Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes
proteins machine-learning deep-learning secondary-structure hhblit psi-blast protein-structure-prediction
Language:C++ 43
Bhattacharya-Lab / PolyFold
An interactive visual simulator for distance-based protein folding
protein-dynamics protein-folding protein-structure-prediction stochastic-optimization
Language:Java 24
lightdock-rust
lightdock / lightdock-rust
A Rust implementation of the LightDock macromolecular docking software
docking protein-structure-prediction protein protein-structure bioinformatics macromolecular-modeling protein-peptide peptide
Language:Rust 23
OkkeVanEck / prospr
Prospr is a universal toolbox for protein structure prediction within the HP-model. The Python package is based on a C++ core, which gives Prospr its high performance. The C++ core is made available as a separate zip file to facilitate high-performance computing applications. The package comes with many prediction algorithms and datasets to use.
bioinformatics computational-science cpp datasets high-performance-computing package protein protein-folding protein-structure-prediction python structure-prediction toolbox
Language:C++ 18
MPI-Dortmund / pymissense
PyMissense creates the pathogenicity plot and modified pdb as shown in the AlphaMissense paper for custom proteins.
deep-learning protein-sequences protein-structure protein-structure-prediction uniprot structural-biology
Language:Python 17
Eryk96 / NetSurfP-3.0
NetSurfP 3.0: Protein secondary structure and relative solvent accessibility prediction
python pytorch protein-structure-prediction docker
Language:Jupyter Notebook 16
DiffPALM
Bitbol-Lab / DiffPALM
Differentiable Pairing using Alignment-based Language Models
bioinformatics language-model machine-learning multiple-sequence-alignment protein-protein-interaction protein-sequences protein-structure-prediction
Language:Jupyter Notebook 13
johnnytam100 / awesome-protein-design
A curated list of awesome protein design research, software and resources.
alphafold alphafold-multimer alphafold2 bioinformatics bioinformatics-tool molecular-biology protein-design protein-function protein-sequence protein-structure structural-bioinformatics structural-biology protein-engineering protein-folding protein-protein-interaction protein-structure-prediction
11
PhilippThoelke / protein-folding
Protein structure prediction using optimization methods from the field of machine learning
protein-folding protein-structure-prediction gradient-descent minimization
Language:Jupyter Notebook 10
Bhattacharya-Lab / QDeep
Distance-based protein model quality estimation using deep ResNets
deep-learning protein-model-quality-estimation protein-scoring-functions protein-structure-prediction
Language:Python 8
taneishi / CB513_dataset
CB513 datasets for Protein Secondary Structure Prediction
deep-learning protein-structure-prediction secondary-structure
Language:Python 8
amckenna41 / protPy
Calculating a range of protein descriptors using their physicochemical, biological and structural properties 🔬.
bioinformatics biological-data-analysis protein-sequences protein-structure protein-structure-prediction pypi python pysar
Language:Python 7
SAMY-ER / Protein-Structure-Prediction
This project aims to solve a simplified version of the Protein Structure Prediction problem, represented as a combinatorial optimization task, using Reinforcement Learning.
reinforcement-learning protein-structure-prediction python machine-learning deep-q-learning
Language:Python 7
CompSoftMatterBiophysics-CityU-HK / Applying-DRL-to-HP-Model-for-Protein-Structure-Prediction
Source code and dataset for 2022 Publication "Applying Deep Reinforcement Learning to the HP Model for Protein Structure Prediction"
deep-reinforcement-learning dqn hp-model lstm optimization protein-structure-prediction
Language:Python 6
libai1943 / Protein-Structure-Optimization-via-Metaheuristics
A balance-evolution artificial bee colony algorithm for protein structure optimization based on a three-dimensional AB off-lattice model
artificial-bee-colony pso protein-structure-prediction protein-structure-optimization metaheuristics numerical-optimization
Language:MATLAB 6
renatawong / quantum-protein-structure-prediction
Quantum algorithms for protein structure prediction. Language: Python (Qiskit). Platform: IBM Quantum's backends and simulators.
quantum-algorithms protein-structure-prediction qiskit protein-folding protein-structure quantum-computing
Language:Jupyter Notebook 6
Bhattacharya-Lab / CASP15
CASP15 performance benchmarking of the state-of-the-art protein structure prediction methods
deep-learning neural-network protein-structure-prediction transformers
5
fpolticelli / tbblab_repository
List of useful resources for the Bioinformatics and Computational Biology field
molecular-dynamics molecular-graphics protein-structure-prediction cheminformatics protein training-materials tutorials
5
Galaxies99 / alpha-protein
Alpha-Protein: Protein Contact-map Prediction Boosted by Attention
attention-mechanism protein-structure-prediction
Language:Python 5
danielvarela / PSPHybridDE
Protein Structure prediction using Hybrid Differential Evolution (HybridDE)
differential-evolution pyrosetta protein-structure-prediction
Language:Python 4
danielvarela / RosettaEvolution
Evolutionary Computation methods applied to protein structure prediction and protein folding modeling with the Rosetta Software Suite
protein-structure-prediction rosetta niching-methods ab-initio-prediction differential-evolution-algorithm mpi niching-algorithms
Language:C++ 4
dohlee / rosettafold-pytorch
An unofficial re-implementation of RoseTTAFold, a three-track deep learning model for protein structure prediction.
bioinformatics computational-biology protein-structure protein-structure-prediction
Language:Python 4
liponan / structure-generator
A machine learning model that builds amino acids into a protein model.
machine-learning structural-biology computational-biology protein protein-sequence protein-structure protein-structure-prediction lstm gcn graph-convolutional-network
Language:Python 4
Bhattacharya-Lab / SPECS
Superposition-based Protein Embedded CA SC score
protein-analysis protein-model-accuracy protein-structure-prediction side-chain-orientation superposition
Language:C++ 3
Galaxies99 / GANcon-pytorch
personal RE-implementation of GANcon paper
generative-adversarial-network protein-structure-prediction
Language:Python 3
psipred / fragfold
Fragment assembly ab initio protein folding
fragment-assembly protein-structure-prediction
Language:C 3

protein-structure-prediction

PaddlePaddle / PaddleHelix

lucidrains / alphafold3-pytorch

RosettaCommons / PyRosetta.notebooks

Urinx / alphafold_pytorch

aqlaboratory / rgn

FreshAirTonight / af2complex

zjunlp / OntoProtein

twoXes / awesome-structural-bioinformatics

psipred / DMPfold

psipred / DMPfold2

mircare / Porter5

Bhattacharya-Lab / PolyFold

lightdock / lightdock-rust

OkkeVanEck / prospr

MPI-Dortmund / pymissense

Eryk96 / NetSurfP-3.0

Bitbol-Lab / DiffPALM

johnnytam100 / awesome-protein-design

PhilippThoelke / protein-folding

Bhattacharya-Lab / QDeep

taneishi / CB513_dataset

amckenna41 / protPy

SAMY-ER / Protein-Structure-Prediction

CompSoftMatterBiophysics-CityU-HK / Applying-DRL-to-HP-Model-for-Protein-Structure-Prediction

libai1943 / Protein-Structure-Optimization-via-Metaheuristics

renatawong / quantum-protein-structure-prediction

Bhattacharya-Lab / CASP15

fpolticelli / tbblab_repository

Galaxies99 / alpha-protein

danielvarela / PSPHybridDE

danielvarela / RosettaEvolution

dohlee / rosettafold-pytorch

liponan / structure-generator

Bhattacharya-Lab / SPECS

Galaxies99 / GANcon-pytorch

psipred / fragfold