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protein-folding

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lucidrains /alphafold2

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

deep-learning artificial-intelligence attention-mechanism protein-folding

UpdatedOct 29, 2022
Python

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

machine-learning ddi deeplearning representation-learning ppi rna-structure-prediction protein-design dti protein-folding protein-structure-prediction biocomputing self-supervised-learning graph-networks protein-docking molecule-design

UpdatedNov 15, 2024
Python

FastFold

hpcaitech /FastFold

Optimizing AlphaFold Training and Inference on GPU Clusters

gpu protein-structure cuda pytorch parallelism protein-folding alphafold2 evoformer habana-gaudi

UpdatedJul 16, 2024
Python

RosettaCommons /PyRosetta.notebooks

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

jupyter-notebook dna rosetta rna-structure-prediction protein-design protein-folding protein-structure-prediction google-colab pyrosetta protein-docking

UpdatedAug 12, 2024
Jupyter Notebook

lucidrains /equiformer-pytorch

Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein folding

deep-learning transformers artificial-intelligence molecules protein-folding attention-mechanisms equivariance

UpdatedDec 17, 2024
Python

lucidrains /invariant-point-attention

Implementation of Invariant Point Attention, used for coordinate refinement in the structure module of Alphafold2, as a standalone Pytorch module

deep-learning artificial-intelligence protein-folding

UpdatedNov 25, 2022
Python

instadeepai /manyfold

🧬 ManyFold: An efficient and flexible library for training and validating protein folding models

python bioinformatics research deep-learning protein-structure protein-folding jax

UpdatedDec 14, 2022
Python

lucidrains /tr-rosetta-pytorch

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

deep-learning artificial-intelligence protein-design protein-folding

UpdatedAug 27, 2021
Python

nf-core /proteinfold

Protein 3D structure prediction pipeline

workflow pipeline nextflow protein-structure protein-sequences protein-folding protein-fold-prediction nf-core alphafold2 colabfold esmfold

UpdatedMar 26, 2025
Nextflow

FrameDiPT

instadeepai /FrameDiPT

FrameDiPT: an SE(3) diffusion model for protein structure inpainting

protein-structure generative-model tcr inpainting protein-folding diffusion-models alphafold2 loop-design

UpdatedJan 22, 2024
Jupyter Notebook

torchmd /torchmd-cg

Example to fit parameters and run CG simulations using TorchMD and Schnet

machine-learning pytorch coarse-grained-molecular-dynamics protein-folding

UpdatedFeb 4, 2022
Jupyter Notebook

prehensilecode /alphafold_singularity

Singularity recipe for AlphaFold

hpc containers slurm singularity high-performance-computing containerization protein-folding alphafold apptainer

UpdatedNov 12, 2024
Python

conradry /prtm

Deep learning for protein science

deep-learning protein-science drug-discovery protein-design protein-folding

UpdatedJun 2, 2024
Python

lucidrains /triangle-multiplicative-module

Implementation of the Triangle Multiplicative module, used in Alphafold2 as an efficient way to mix rows or columns of a 2d feature map, as a standalone package for Pytorch

deep-learning artificial-intelligence protein-folding

UpdatedAug 3, 2021
Python

Bhattacharya-Lab /PolyFold

An interactive visual simulator for distance-based protein folding

protein-dynamics stochastic-optimization protein-folding protein-structure-prediction

UpdatedMar 1, 2021
Java

aws-samples /aws-rosettafold

Infrastructure template and Jupyter notebooks for running RoseTTAFold on AWS Batch.

aws deep-learning hpc aws-batch protein-folding alphafold2 rosettafold

UpdatedFeb 24, 2022
Python

thuxugang /opus_fold

OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling

protein-secondary-structure protein-folding protein-scoring-functions protein-contact-map opus-fold protein-strucutre-prediction protein-side-chain-modeling protein-torsion-angles protein-potential-functions

UpdatedMay 4, 2020

MasterMSM

BioKT /MasterMSM

Python package for generating Markov state models

molecular-dynamics markov-state-model protein-folding

UpdatedJul 27, 2022
Python

macrocosm-os /folding

Decentralized Protein Folding Bittensor Subnet

crypto decentralized origami protein-folding bittensor

UpdatedMar 26, 2025
Python

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.

python package bioinformatics cpp toolbox protein high-performance-computing datasets computational-science structure-prediction protein-folding protein-structure-prediction

UpdatedFeb 10, 2025
C++

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