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179

1.4k

mit

46

Implementation of Alphafold 3 from Google Deepmind in Pytorch

transformers deep-learning denoising-diffusion attention-mechanisms artificial-intelligence protein-structure-prediction

Created 2024-05-08

1,002 commits to main branch, last one 3 months ago

PaddleHelix PaddlePaddle

229

1.1k

other

25

Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

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

Created 2020-11-21

864 commits to dev branch, last one 5 months ago

PyRosetta.notebooks RosettaCommons

159

559

mit

329

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

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

Created 2019-05-24

595 commits to master branch, last one 8 months ago

alphafold_pytorch Urinx

90

395

apache-2.0

13

An implementation of the DeepMind's AlphaFold based on PyTorch for research

casp13 alphafold deep-learning contact-prediction structure-prediction pytorch-implementation protein-structure-prediction

Created 2020-02-11

4 commits to master branch, last one 5 years ago

DL4Proteins-notebooks Graylab

50

358

mit

6

Colab Notebooks covering deep learning tools for biomolecular structure prediction and design

rna-design deep-learning language-model protein-design neural-networks protein-docking small-molecules diffusion-models jupyter-notebooks graph-neural-networks protein-structure-prediction convolutional-neural-networks

Created 2024-09-04

95 commits to main branch, last one 11 days ago

af2complex FreshAirTonight

19

159

unknown

6

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.

alphafold2 deep-learning bioinformatics protein-complexes protein-protein-docking protein-protein-interaction protein-structure-prediction

Created 2021-11-07

119 commits to main branch, last one 7 months ago

OntoProtein zjunlp

22

146

mit

7

[ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding

nlp bert iclr protein pytorch iclr2022 ontoprotein pretraining gene-ontology knowledge-graph pretrained-models protein-pretraining protein-function-prediction protein-protein-interaction protein-structure-prediction

Created 2021-12-18

52 commits to main branch, last one about a month ago

Dense-Homolog-Retrieval ml4bio

6

102

bsd-3-clause

4

Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval

protein alphafold dense-retrieval homology-search msa-construction protein-language-model protein-structure-prediction

Created 2022-10-16

15 commits to main branch, last one 7 months ago

awesome-structural-bioinformatics twoXes

10

70

unknown

2

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.

Created 2021-03-21

175 commits to main branch, last one about a year ago

DMPfold psipred

16

57

gpl-3.0

6

De novo protein structure prediction using iteratively predicted structural constraints

resnet deep-learning protein-sequence protein-structure protein-structure-prediction

Created 2019-01-10

182 commits to master branch, last one 3 years ago

DMPfold2 psipred

12

51

gpl-3.0

5

Fast and accurate protein structure prediction

end-to-end deep-learning multiple-sequence-alignment protein-structure-prediction

Created 2020-09-07

101 commits to master branch, last one 2 months ago