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awesome-protein-representation-learning LirongWu

71

614

mit

23

Awesome Protein Representation Learning

protein-modeling protein-embedding protein-sequences representation-learning protein-representation-learning

Created 2022-10-05

69 commits to main branch, last one 5 days ago

GearNet DeepGraphLearning

27

273

mit

10

GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)

pre-training graph-neural-networks protein-representation-learning

Created 2022-07-05

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

protein-sequence-embedding-iclr2019 tbepler

75

258

other

11

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

pytorch deep-learning language-model protein-modeling protein-sequence protein-embedding protein-structure recurrent-neural-networks protein-representation-learning

Created 2019-02-22

7 commits to master branch, last one 3 years ago

MAPE-PPI LirongWu

44

250

mit

2

Code for ICLR 2024 (Spotlight) paper "MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding"

codebook vocabulary ppi-networks masked-modeling microenvironment protein-embedding protein-protein-interaction protein-representation-learning

Created 2024-01-24

9 commits to main branch, last one 5 months ago

ProtFlash ISYSLAB-HUST

3

100

mit

2

ProtFlash: A lightweight protein language model

bioinformatics protein-sequence pretrained-models protein-embeddings protein-language-model protein-representation-learning

Created 2022-09-22

17 commits to main branch, last one 8 months ago

Protein_Redesign HySonLab

5

39

mit

4

Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models

protein ligand-binding protein-design diffusion-models equivariant-network protein-representation-learning

Created 2024-02-13

23 commits to main branch, last one 11 days ago

SiamDiff DeepGraphLearning

5

39

unknown

4

Code for Pre-training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction (https://arxiv.org/abs/2301.12068)

protein pre-training protein-protein-interaction protein-representation-learning

Created 2023-07-06

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

PST BorgwardtLab

1

32

bsd-3-clause

4

Protein Structure Transformer (PST): Endowing pretrained protein language models with structural knowledge

graph-transformer protein-structure evolutionary-scale-modeling protein-representation-learning

Created 2023-12-27

61 commits to main branch, last one 9 months ago

PSC-CPI LirongWu

2

25

mit

2

Code for AAAI 2024 paper "PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction"

protein-modeling contrastive-learning compound-protein-interaction protein-representation-learning

Created 2023-12-14

3 commits to main branch, last one 8 months ago