Research graph
References from SpatialPPIv2: Enhancing protein–protein interaction prediction through graph neural networks with protein language models. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1016/j.csbj.2022.08.070
10.1016/j.csbj.2022.08.070 · External reference
Recent advances in protein–protein interactions
10.3390/ijms24021282 · 2023 · External reference
State-of-the-art computational methods to predict protein–protein interactions with high accuracy and coverage
10.1002/pmic.202200292 · 2023 · External reference
TT3D: leveraging precomputed protein 3D sequence models to predict protein–protein interactions
10.1093/bioinformatics/btad663 · 2023 · External reference
Identification of all-against-all protein–protein interactions based on deep hash learning
10.1186/s12859-022-04811-x · 2022 · External reference
10.1021/acs.jcim.7b00028
10.1021/acs.jcim.7b00028 · External reference
10.1016/j.cels.2021.08.010
10.1016/j.cels.2021.08.010 · External reference
Topsy-Turvy: integrating a global view into sequence-based PPI prediction
10.1093/bioinformatics/btac258 · 2022 · External reference
An exhaustive review of computational prediction techniques for PPI sites, protein locations, and protein functions
10.1007/s13721-023-00427-0 · 2023 · External reference
Structure-aware protein–protein interaction site prediction using deep graph convolutional network
10.1093/bioinformatics/btab643 · 2021 · External reference
10.1038/s41467-023-36736-1
10.1038/s41467-023-36736-1 · External reference
Learning spatial structures of proteins improves protein–protein interaction prediction
10.1093/bib/bbab558 · 2021 · External reference
Unresolved reference
2021 · External reference
A deep learning architecture for metabolic pathway prediction
10.1093/bioinformatics/btz954 · 2019 · External reference
Graph neural network for protein–protein interaction prediction: a comparative study
10.3390/molecules27186135 · 2022 · External reference
Benchmark evaluation of protein–protein interaction prediction algorithms
10.3390/molecules27010041 · 2021 · External reference
10.1038/s41586-021-03819-2
10.1038/s41586-021-03819-2 · External reference
Critical assessment of methods of protein structure prediction (CASP)—progress and new directions in round XIV
2021 · External reference
10.1038/s41586-024-07487-w
10.1038/s41586-024-07487-w · External reference
10.1126/science.ade2574
10.1126/science.ade2574 · External reference
Improved prediction of protein-protein interactions using AlphaFold2
10.1038/s41467-022-29480-5 · 2022 · External reference
10.1016/j.csbj.2024.03.009 · Admitted local publication
10.1101/2021.10.04.463034
10.1101/2021.10.04.463034 · External reference
10.1101/2024.07.17.603980
10.1101/2024.07.17.603980 · External reference
DIPS-plus: the enhanced database of interacting protein structures for interface prediction
10.1038/s41597-023-02409-3 · 2023 · External reference
ProteinFlow: an advanced framework for feature engineering in protein data analysis
10.1002/bit.28812 · 2024 · External reference
Unresolved reference
External reference
10.1107/s0907444902003451
10.1107/s0907444902003451 · External reference
10.1038/s41586-021-03828-1
10.1038/s41586-021-03828-1 · External reference
Improved cytokine–receptor interaction prediction by exploiting the negative sample space
10.1186/s12859-020-03835-5 · 2020 · External reference
10.1016/j.ymeth.2012.07.028
10.1016/j.ymeth.2012.07.028 · External reference
Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis
10.1093/nar/gkt1079 · 2013 · External reference
10.1073/pnas.0735871100
10.1073/pnas.0735871100 · External reference
ProtTrans: toward understanding the language of life through self-supervised learning
10.1109/tpami.2021.3095381 · 2021 · External reference
Unresolved reference
2019 · External reference
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
10.1073/pnas.2016239118 · 2021 · External reference
Integration of pre-trained protein language models into geometric deep learning networks
10.1038/s42003-023-05133-1 · 2023 · External reference
Graph-BERT and language model-based framework for protein–protein interaction identification
10.1038/s41598-023-31612-w · 2023 · External reference
iAlign: a method for the structural comparison of protein–protein interfaces
10.1093/bioinformatics/btq404 · 2010 · External reference
Protein residue contacts and prediction methods
10.1007/978-1-4939-3572-7_24 · 2016 · External reference
The importance of being negative
10.1038/nmeth0110-10b · 2009 · External reference
IntAct: an open source molecular interaction database
10.1093/nar/gkh052 · 2003 · External reference
BioGRID: a general repository for interaction datasets
10.1093/nar/gkj109 · 2005 · External reference
Unresolved reference
External reference
Protein–protein interaction prediction model based on ProtBERT-BiGRU-attention
10.1089/cmb.2023.0297 · 2024 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
UniProt: the universal protein knowledgebase
10.1093/nar/gkh131 · 2003 · External reference
10.1038/s41467-022-32007-7
10.1038/s41467-022-32007-7 · External reference
SGPPI: structure-aware prediction of protein–protein interactions in rigorous conditions with graph convolutional network
10.1093/bib/bbad020 · 2023 · External reference
Unresolved reference
External reference
Prediction of protein–protein interaction using graph neural networks
10.1038/s41598-022-12201-9 · 2022 · External reference
Benchmarking graph neural networks
2022 · External reference
10.1101/2020.12.15.422761
10.1101/2020.12.15.422761 · External reference
Unresolved reference
External reference
Unresolved reference
2018 · External reference
10.1371/journal.pone.0008514
10.1371/journal.pone.0008514 · External reference
Improved prediction of protein–protein interactions using novel negative samples, features, and an ensemble classifier
10.1016/j.artmed.2017.03.001 · 2017 · External reference
10.1073/pnas.97.24.13203
10.1073/pnas.97.24.13203 · External reference
