protein-protein-interaction

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

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

UpdatedJun 20, 2024
Python

octavian-ganea /equidock_public

Star243

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

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

UpdatedSep 22, 2023
Roff

FreshAirTonight /af2complex

Star162

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

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

UpdatedSep 8, 2024
Python

zjunlp /OntoProtein

Star148

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

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

UpdatedMar 10, 2025
Python

DeepRank /deeprank

Star145

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

pytorch docking protein-protein-interaction 3d-cnn

UpdatedNov 28, 2023
Python

Thinklab-SJTU /awesome-molecular-docking

Star102

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

machine-learning awesome bioinformatics deep-learning binding protein-ligand-docking molecular-dynamics generative-model drug-discovery awesome-list drug-design optimal-transport protein-protein-interaction drug-protein-interactions geometric-deep-learning molecular-docking paper-list equivariant-representations ai-aided-drug-discovery drugai

UpdatedFeb 23, 2023

anton-bushuiev /PPIRef

Star94

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

machine-learning proteins datasets protein-protein-interaction

UpdatedApr 28, 2025
Jupyter Notebook

Bindwell /APPT

Star90

Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!

machine-learning bioinformatics protein-sequences protein-protein-interaction binding-affinity

UpdatedFeb 18, 2025
Python

sbl-sdsc /mmtf-pyspark

Star68

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

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

UpdatedMar 27, 2023
Python

akiyamalab /MEGADOCK

Star63

An ultra-high-performance protein-protein docking for heterogeneous supercomputers

bioinformatics gpu cuda fftw protein-protein-interaction

UpdatedDec 10, 2023
C++

sbl-sdsc /mmtf-workshop-2018

Star60

Structural Bioinformatics Training Workshop & Hackathon 2018

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

UpdatedMay 17, 2022
Jupyter Notebook

sigven /oncoEnrichR

Star51

Explore the cancer relevance of your gene list

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

UpdatedFeb 28, 2025
R

dwhswenson /contact_map

Star45

Contact map analysis for biomolecules; based on MDTraj

bioinformatics molecular-dynamics computational-biology biochemistry protein-protein-interaction protein-ligand-interactions

UpdatedDec 20, 2024
Python

ncbi /BioConceptVec

Star41

text-mining deep-learning word-embeddings protein-protein-interaction biomedical-text-mining biomedical-concept-embeddings

UpdatedFeb 26, 2020
Jupyter Notebook

DeepGraphLearning /SiamDiff

Star41

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

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

UpdatedJul 9, 2023
Python

LirongWu /Prompt-DDG

Star41

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

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