protein-protein-interaction

There are 7 repositories under protein-protein-interaction topic.

kexinhuang12345 / DeepPurpose
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
drug-repurposing deep-learning drug-target-interactions toolkit covid19 virtual-screening drug-discovery ppi ddi dti-prediction drug-property-prediction protein-function-prediction repurposing-drugs qsar side-effects drug-drug-interaction protein-protein-interaction drug-target-interaction bioinformatics
Language:Jupyter Notebook 903
lightdock
lightdock / lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
protein protein-structure protein-protein-interaction protein-docking swarm-intelligence glowworm-swarm-optimization protein-dna-interactions peptides dna docking artificial-intelligence protein-design proteomics structural-biology structural-bioinformatics bioinformatics bioinformatics-tool chemistry molecular-biology molecular-structures
Language:Python 270
octavian-ganea / equidock_public
EquiDock: geometric deep learning for fast rigid 3D protein-protein docking
geometry proteins protein-protein-interaction docking graphneuralnetwork deeplearning equivariant-network equivariance equivariant-representations drugdiscovery drug-discovery
Language:Roff 223
DeepRank / deeprank
This repository has been integrated in https://github.com/DeepRank/deeprank2
3d-cnn protein-protein-interaction docking pytorch
Language:Python 147
LirongWu / MAPE-PPI
Code for ICLR 2024 (Spotlight) paper "MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding"
codebook masked-modeling microenvironment ppi-networks protein-embedding protein-protein-interaction protein-representation-learning vocabulary
Language:Python 133
zjunlp / OntoProtein
[ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding
protein-protein-interaction gene-ontology protein-pretraining protein-function-prediction protein-structure-prediction knowledge-graph protein ontoprotein bert nlp pytorch pretrained-models pretraining iclr iclr2022
Language:Python 132
af2complex
FreshAirTonight / af2complex
Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
bioinformatics deep-learning alphafold2 protein-complexes protein-protein-interaction protein-structure-prediction protein-protein-docking
Language:Python 128
awesome-molecular-docking
Thinklab-SJTU / awesome-molecular-docking
We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.
ai-aided-drug-discovery awesome drug-discovery molecular-docking paper-list bioinformatics machine-learning protein-protein-interaction molecular-dynamics binding generative-model drug-design equivariant-representations drug-protein-interactions geometric-deep-learning awesome-list deep-learning optimal-transport protein-ligand-docking drugai
84
sbl-sdsc / mmtf-pyspark
Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.
pyspark binder protein-data-bank jupyter-notebook jupyter machine-learning scientific-computing big-data protein-structure protein-sequences protein-protein-interaction protein-ligand-interactions apache-spark
Language:Python 67
sbl-sdsc / mmtf-workshop-2018
Structural Bioinformatics Training Workshop & Hackathon 2018
pyspark binder protein-data-bank jupyter-notebook jupyter machine-learning big-data protein-protein-interaction protein-ligand-interactions 3d-visualization apache-spark workshop-materials hackathon
Language:Jupyter Notebook 57
sigven / oncoEnrichR
Cancer-dedicated gene set interpretation
cancer high-throughput-screening tcga-data report-generator protein-protein-interaction co-expression disease-gene-association crispr-target proteins genesets prioritization protein-complexes cancer-survival functional-enrichment-analysis tissue-enrichment-analysis pathway-enrichment-analysis cancer-hallmark-evidence
Language:R 48
akiyamalab / MEGADOCK
An ultra-high-performance protein-protein docking for heterogeneous supercomputers
bioinformatics gpu fftw protein-protein-interaction cuda
Language:C++ 42
ncbi / BioConceptVec
biomedical-concept-embeddings biomedical-text-mining deep-learning text-mining word-embeddings protein-protein-interaction
Language:Jupyter Notebook 40
dwhswenson / contact_map
Contact map analysis for biomolecules; based on MDTraj
bioinformatics biochemistry protein-protein-interaction molecular-dynamics protein-ligand-interactions computational-biology
Language:Python 38
DeepGraphLearning / SiamDiff
Code for Pre-training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction (https://arxiv.org/abs/2301.12068)
pre-training protein protein-protein-interaction protein-representation-learning
Language:Python 31
anton-bushuiev / PPIRef
Working with protein-protein interactions in 3D
datasets machine-learning protein-protein-interaction proteins
Language:Jupyter Notebook 28
sbl-sdsc / mmtf-genomics
Methods for mapping genomic data onto 3D protein structure.
genomics mutations protein-structure protein-data-bank dbsnp protein-protein-interaction protein-ligand-interactions protein-drug-interactions pyspark mmtf-pyspark binder cyverse
Language:Jupyter Notebook 27
DongqiFu / DPPIN
DPPIN: A Biological Repository of Dynamic Protein-Protein Interaction Network Data, IEEE BigData' 2022
graph-dataset graph-generation protein-protein-interaction
Language:Python 25
lightdock-python2.7
lightdock / lightdock-python2.7
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
gso pdb swarm-intelligence scientific-computing protein-protein-docking protein-protein protein-protein-interaction protein-structure swarm protein docking simulation dna peptides anm proteins protein-design bioinformatics protein-docking-framework
Language:C++ 25
EureKaZhu / DiffAffinity
Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model (NeurIPS 2023 Poster)
ai4science diffusion-models protein-protein-interaction
Language:Jupyter Notebook 22
sbl-sdsc / mmtf-spark
Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.
protein-structure protein-data-bank protein-sequences protein-ligand-interactions protein-protein-interaction machine-learning big-data apache-spark scientific-computing
Language:Java 22
dvklopfenstein / ReactomePy
Explore biomolecular pathways in Reactome from the command-line or a Python script
reactome reactome-pathway biological-networks molecular-biology pathway-enrichment-analysis pathway-analysis biotechnology biotech bioinformatics bioinformatics-pipeline bioinformatics-analysis bioinformatics-scripts bioinformatics-tool pathway-models protein-protein-interaction
Language:Python 21
DeepRank / DeepRank-GNN-esm
Graph Network for protein-protein interface including language model features
deep-learning graph-networks language-model protein-protein-interaction scoring interface-classification utrecht-university
Language:Python 20
wajidarshad / LUPI-SVM
SVM with Learning Using Privileged Information (LUPI) framework
svm artificial-intelligence pegasos machine-learning protein-protein-interaction proteomics pattern-recognition stochastic-gradient-descent lupi
Language:Python 20
LPDI-EPFL / FunFolDesData
Rosetta FunFolDes – a general framework for the computational design of functional proteins.
protein-design rosetta publication-data functional-protein-design protein-structure protein-protein-interaction structural-biology
Language:Scala 18
AspirinCode / iPPIGAN
De novo molecular design with deep molecular generative models for protein-protein interaction(PPI) inhibitors
deep-molecular-generative-models protein-protein-interaction drug-likeness qed qeppi ppi-inhibitor drug-discovery ppi
Language:Jupyter Notebook 17
ikmb / amino_acid_encoding_deep_learning_applications
The repository contains all the code for the paper amino acid encoding using deep learning application
hla protein-protein-interaction sequence-em amino-acid amino-acid-encoding tensorflow2 convolutional-neural-networks long-short-term-memory
Language:Python 17
zhuango / KAN
An implementation of Knowledge-aware attention networks (KAN) for protein-protein extraction task
attention protein-protein-interaction prior-knowledge
Language:Python 15
aedera / anc2vec
Unsupervised neural network for learning embeddings of GO terms.
embeddings obo go gene-ontology autoencoder neural-network protein-protein-interaction protein-function
Language:Python 14
DiffPALM
Bitbol-Lab / DiffPALM
Differentiable Pairing using Alignment-based Language Models
bioinformatics language-model machine-learning multiple-sequence-alignment protein-protein-interaction protein-sequences protein-structure-prediction
Language:Jupyter Notebook 14
gdocking / gdock
Protein-Protein Docking using Genetic Algorithm
protein-docking docking bioinformatics structural-biology computational-biology protein protein-structure protein-protein-interaction structural-bioinformatics genetic-algorithm deap chemistry
Language:Python 13
haddocking / haddocking.github.io
Webpage of the Bonvinlab @ Utrecht University and HADDOCK software
utrecht-university research education software integrative-modeling modeling protein-protein-interaction structural-bioinformatics structural-biology
Language:HTML 13
unistbig / netGO
R/Shiny package for network-integrated pathway enrichment analysis
r network-analysis netgo shinyapps protein-protein-interaction enrichment-analysis
Language:R 13
Wang-Lin-boop / PPI-Miner
A Motif-Based PPI Searching Pipeline for PPI Mining and Protein Design
protein-design protein-protein-interaction molecule-glue
Language:Shell 13
louadi / NEASE
A network-based approach for exon set enrichment
network-analysis statistics bioinformatics-tool protein-protein-interaction alternative-splicing rna-seq transcriptomics
Language:Python 12
YeongHyeon / PIPGCN-TF2
Unofficial TensorFlow implementation of Protein Interface Prediction using Graph Convolutional Networks.
graph-neural-networks graph-neural-network graph-convolutional-networks graph-convolutional-network protein-protein-interaction protein prediction
Language:Python 12