Search Results - RepositoryStats

273

959

bsd-3-clause

31

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

ddi ppi qsar covid19 toolkit side-effects deep-learning bioinformatics drug-discovery dti-prediction drug-repurposing repurposing-drugs virtual-screening drug-drug-interaction drug-target-interaction drug-property-prediction drug-target-interactions protein-function-prediction protein-protein-interaction

Created 2020-03-19

529 commits to master branch, last one 3 months ago

lightdock lightdock

40

301

gpl-3.0

12

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

Created 2019-09-27

488 commits to master branch, last one 8 months ago

MAPE-PPI LirongWu

39

232

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 3 months ago

equidock_public octavian-ganea

58

231

mit

8

EquiDock: geometric deep learning for fast rigid 3D protein-protein docking

docking geometry proteins deeplearning equivariance drugdiscovery drug-discovery graphneuralnetwork equivariant-network equivariant-representations protein-protein-interaction

Created 2022-02-04

20 commits to main branch, last one 2 years ago

af2complex FreshAirTonight

19

147

unknown

7

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 20 days ago

deeprank DeepRank

27

145

apache-2.0

14

This repository has been integrated in https://github.com/DeepRank/deeprank2

3d-cnn docking pytorch protein-protein-interaction

This repository has been archived (exclude archived)

Created 2017-09-12

1,129 commits to master branch, last one 10 months ago

OntoProtein zjunlp

22

141

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

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

awesome-molecular-docking Thinklab-SJTU

6

89

mit

3

We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.

Created 2022-12-10

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

PPIRef anton-bushuiev

8

81

mit

3

Dataset and package for working with protein-protein interactions in 3D

datasets proteins machine-learning protein-protein-interaction

Created 2023-10-16

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

mmtf-pyspark sbl-sdsc

27

67

apache-2.0

8

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

binder jupyter pyspark big-data apache-spark jupyter-notebook machine-learning protein-data-bank protein-sequences protein-structure scientific-computing protein-ligand-interactions protein-protein-interaction

Created 2017-05-11

1,752 commits to master branch, last one about a year ago

mmtf-workshop-2018 sbl-sdsc

34

57

apache-2.0

5

Structural Bioinformatics Training Workshop & Hackathon 2018

binder jupyter pyspark big-data hackathon apache-spark 3d-visualization jupyter-notebook machine-learning protein-data-bank workshop-materials protein-ligand-interactions protein-protein-interaction

Created 2018-04-23

137 commits to master branch, last one 2 years ago

SaprotHub westlake-repl

6

56

mit

3

SaprotHub: Making Protein Modeling Accessible to All Biologists

nlp saprot saprothub protein-design protein-fitness universal-model foundation-models protein-structure protein-language-model protein-function-prediction protein-protein-interaction

Created 2024-05-02

425 commits to main branch, last one 3 days ago

oncoEnrichR sigven

10

49

mit

6

Explore the cancer relevance of your gene list

cancer genesets proteins tcga-data co-expression crispr-target prioritization cancer-survival report-generator protein-complexes cancer-hallmark-evidence disease-gene-association high-throughput-screening tissue-enrichment-analysis pathway-enrichment-analysis protein-protein-interaction functional-enrichment-analysis

Created 2019-11-21

320 commits to main branch, last one 19 days ago

SiamDiff DeepGraphLearning

5

38

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

Prompt-DDG LirongWu

2

27

mit

3

Code for ICML 2024 paper "Learning to Predict Mutational Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning"

prompt-leaning antibody-optimization protein-protein-interaction mutational-effect-prediction

Created 2024-05-06

8 commits to main branch, last one 3 months ago

DiffAffinity EureKaZhu

2

27

unknown

2

Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model (NeurIPS 2023 Poster)

ai4science diffusion-models protein-protein-interaction

Created 2023-08-07

20 commits to main branch, last one 9 months ago

DeepRank-GNN-esm DeepRank

8

25

apache-2.0

6

Graph Network for protein-protein interface including language model features

scoring deep-learning graph-networks language-model utrecht-university interface-classification protein-protein-interaction

Created 2023-06-15

109 commits to main branch, last one 6 months ago