Predicting Protein–Protein Interactions from the Molecular to the Proteome Level

Cytoscape: A software Environment for integrated models of biomolecular interaction networks

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The Protein Data Bank

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Book Review: Pattern Recognition and Machine Learning

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STRING v10: protein–protein interaction networks, integrated over the tree of life

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Alternative isoform regulation in human tissue transcriptomes

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A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

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STRING v9.1: protein-protein interaction networks, with increased coverage and integration

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A comprehensive two-hybrid analysis to explore the yeast protein interactome

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Human Protein Reference Database--2009 update

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Artificial intelligence to deep learning: machine intelligence approach for drug discovery

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Deciphering molecular interactions by proximity labeling

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Network-based prediction of protein interactions

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Protein Assembly by Design

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Improving protein-protein interactions prediction accuracy using XGBoost feature selection and stacked ensemble classifier

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New insights into protein–protein interaction modulators in drug discovery and therapeutic advance

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High-strength hydrogels: Fabrication, reinforcement mechanisms, and applications

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Bioadhesion in the oral cavity and approaches for biofilm management by surface modifications

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Learning functional properties of proteins with language models

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A survey on computational models for predicting protein–protein interactions

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Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates

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μMap-Red: Proximity Labeling by Red Light Photocatalysis

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Protein–protein interactions: detection, reliability assessment and applications

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Evolution of resilience in protein interactomes across the tree of life

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The increasing dynamic, functional complexity of bio-interface materials

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Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis

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Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery

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Network analysis and in silico prediction of protein–protein interactions with applications in drug discovery

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Extracellular Vesicles Produced by the Probiotic Propionibacterium freudenreichii CIRM-BIA 129 Mitigate Inflammation by Modulating the NF-κB Pathway

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Current advances in photocatalytic proximity labeling

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A genetically encoded photoproximity labeling approach for mapping protein territories

Hananya, N., Ye, X., Koren, S., & Muir, T. W. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2219339120 · Cited by 86

Dysregulation of Signaling Pathways Due to Differentially Expressed Genes From the B-Cell Transcriptomes of Systemic Lupus Erythematosus Patients – A Bioinformatics Approach

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Plant proteomic research for improvement of food crops under stresses: a review

Mustafa, G., & Komatsu, S. (2021) · Molecular Omics · doi:10.1039/d1mo00151e · Cited by 63

Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins

Lima, D. B., Melchior, J., Morris, J. C., Barbosa, V. C., Chamot‐Rooke, J., Fioramonte, M., Souza, T. A. C. B., Fischer, J. D. S. D. G., Gozzo, F. C., Carvalho, P. C., et al. (2018) · Nature Protocols · doi:10.1038/nprot.2017.113 · Cited by 62

Understanding Ethanol Tolerance Mechanism in Saccharomyces cerevisiae to Enhance the Bioethanol Production: Current and Future Prospects

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Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments

Lamprakis, C., Andreadelis, I., Manchester, J. I., Velez‐Vega, C., Duca, J. S., & Cournia, Z. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.0c00507 · Cited by 59

Nanopore Detection Using Supercharged Polypeptide Molecular Carriers

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Studying protein–protein interactions: Latest and most popular approaches

Akbarzadeh, S., Coşkun, Ö., & Günçer, B. (2024) · Journal of Structural Biology · doi:10.1016/j.jsb.2024.108118 · Cited by 60

Mitochondrial permeability transition pore: Back to the drawing board

Chinopoulos, C. (2017) · Neurochemistry International · doi:10.1016/j.neuint.2017.06.010 · Cited by 57

Exploring protein-protein interactions at the proteome level

Elhabashy, H., Merino, F., Alva, V., Kohlbacher, O., & Lupas, A. N. (2022) · Structure · doi:10.1016/j.str.2022.02.004 · Cited by 57

Efficient Classification of Hot Spots and Hub Protein Interfaces by Recursive Feature Elimination and Gradient Boosting

Lin, X., Zhang, X., & Xu, X. (2019) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2019.2931717 · Cited by 58

Exploring the potential of 3D Zernike descriptors and SVM for protein–protein interface prediction

Daberdaku, S., & Ferrari, C. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2043-3 · Cited by 57

SGPPI: structure-aware prediction of protein–protein interactions in rigorous conditions with graph convolutional network

Huang, Y., Wuchty, S., Zhou, Y., & Zhang, Z. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad020 · Cited by 51

Using Interactome Big Data to Crack Genetic Mysteries and Enhance Future Crop Breeding

Wu, L., Han, L., Li, Q., Wang, G., Zhang, H., & Li, L. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.12.012 · Cited by 49

Disulfide Click Reaction for Stapling of S‐terminal Peptides

Yu, Q., Bai, L., & Jiang, X. (2023) · Angewandte Chemie International Edition · doi:10.1002/anie.202314379 · Cited by 48

Studying protein–protein interactions: progress, pitfalls and solutions

Hayes, S. L., Malacrida, B., Bailey‐Whyte, M., & Kiely, P. A. (2016) · Biochemical Society Transactions · doi:10.1042/bst20160092 · Cited by 47

Quantum Chemistry Simulation of Biological Molecules

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Assessment of community efforts to advance network-based prediction of protein–protein interactions

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The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein–Protein Interactions (PPIs)

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Mapping the SARS-CoV-2–Host Protein–Protein Interactome by Affinity Purification Mass Spectrometry and Proximity-Dependent Biotin Labeling: A Rational and Straightforward Route to Discover Host-Directed Anti-SARS-CoV-2 Therapeutics

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Transfer learning in proteins: evaluating novel protein learned representations for bioinformatics tasks

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Prediction of protein-protein interactions based on ensemble residual convolutional neural network

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Bioorthogonal masked acylating agents for proximity-dependent RNA labelling

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PPISB: A Novel Network-Based Algorithm of Predicting Protein-Protein Interactions With Mixed Membership Stochastic Blockmodel

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Application of docking methodologies to modeled proteins

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Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network

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DeepHomo2.0: improved protein–protein contact prediction of homodimers by transformer-enhanced deep learning

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Predicting Biomedical Interactions With Higher-Order Graph Convolutional Networks

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Targeting Protein–Protein Interfaces with Peptides: The Contribution of Chemical Combinatorial Peptide Library Approaches

Monti, A., Vitagliano, L., Caporale, A., Ruvo, M., & Doti, N. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24097842 · Cited by 43

Lighting the way: Compelling open questions in photosynthesis research

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PlaPPISite: a comprehensive resource for plant protein-protein interaction sites

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Chemically functionalized conical PET nanopore for protein detection at the single-molecule level

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Neuropilin-1 is a glial cell line-derived neurotrophic factor receptor in glioblastoma

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Dynamic protein interfaces and conformational landscapes of membrane protein complexes

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Protein interaction networks: centrality, modularity, dynamics, and applications

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Protein-fragment complementation assays for large-scale analysis of protein–protein interactions

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Few shot learning for phenotype-driven diagnosis of patients with rare genetic diseases

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Protein–protein interactions of human glyoxalase II: findings of a reliable docking protocol

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Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing

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Exploring protein‐protein interactions using the site‐identification by ligand competitive saturation methodology

Yu, W., Jo, S., Lakkaraju, S. K., Weber, D. J., & MacKerell, A. D. (2018) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25650 · Cited by 35

Improved measures for evolutionary conservation that exploit taxonomy distances

Malhis, N., Jones, S. J. M., & Gsponer, J. A. (2019) · Nature Communications · doi:10.1038/s41467-019-09583-2 · Cited by 34

Mutational landscape of K-Ras substitutions at 12th position-a systematic molecular dynamics approach

Kumar, S. U., Bithia, R., Kumar, D. T., Doss, C. G. P., & Zayed, H. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1830177 · Cited by 32

Improving protein–protein interactions prediction accuracy using protein evolutionary information and relevance vector machine model

An, J., Meng, F., You, Z., Chen, X., Yan, G., & Hu, J. (2016) · Protein Science · doi:10.1002/pro.2991 · Cited by 32

A survey of computational methods in protein–protein interaction networks

Rasti, S., & Vogiatzis, C. (2018) · Annals of Operations Research · doi:10.1007/s10479-018-2956-2 · Cited by 36

Protein Interaction Network Reconstruction Through Ensemble Deep Learning With Attention Mechanism

Li, F., Zhu, F., Ling, X., & Liu, Q. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.00390 · Cited by 31

Molecular basis for protein–protein interactions

Seychell, B. C., & Beck, T. (2021) · Beilstein Journal of Organic Chemistry · doi:10.3762/bjoc.17.1 · Cited by 32

A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach

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Rational Prediction of PROTAC-Compatible Protein–Protein Interfaces by Molecular Docking

Pereira, G. P., Jiménez‐García, B., Pellarin, R., Launay, G., Wu, S., Martin, J., & Souza, P. C. T. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01154 · Cited by 32

Structure-based prediction of host–pathogen protein interactions

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A Proximity Mapping Journey into the Biology of the Mammalian Centrosome/Cilium Complex

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Specific inhibition of the Survivin–CRM1 interaction by peptide-modified molecular tweezers

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Precise protein assembly of array structures

Yang, G., Wu, L., Chen, G., & Jiang, M. (2016) · Chemical Communications · doi:10.1039/c6cc04190f · Cited by 29

Prediction of Hot Regions in PPIs Based on Improved Local Community Structure Detecting

Lin, X., & Zhang, X. (2018) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2018.2793858 · Cited by 29

Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom Molecular Dynamics Simulations, Confirming a Stepwise Association Process for Native Protein–Protein Interactions

Li, Z., & Buck, M. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.9b00195 · Cited by 29

NCI-ELMO: A New Method To Quickly and Accurately Detect Noncovalent Interactions in Biosystems

Arias‐Olivares, D., Wieduwilt, E. K., Contreras‐García, J., & Genoni, A. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.9b00658 · Cited by 29

Quantitative Yeast–Yeast Two Hybrid for the Discovery and Binding Affinity Estimation of Protein–Protein Interactions

Bacon, K. B., Blain, A., Bowen, J., Burroughs, M. R., McArthur, N., Menegatti, S., & Rao, B. M. (2021) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00472 · Cited by 29

Crystal structures of eukaryote glycosyltransferases reveal biologically relevant enzyme homooligomers

Harrus, D., Kellokumpu, S., & Glumoff, T. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2659-x · Cited by 28

Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA

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Efficiently Predicting Hot Spots in PPIs by Combining Random Forest and Synthetic Minority Over-Sampling Technique

Zhang, X., Lin, X., Zhao, J., Huang, Q., & Xu, X. (2018) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2018.2871674 · Cited by 27

Head perturbations during walking while viewing a head-fixed target.

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How Can Interleukin-1 Receptor Antagonist Modulate Distinct Cell Death Pathways?

Spinello, A., Vecile, E., Abbate, A., Dobrina, A., & Magistrato, A. (2018) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.8b00565 · Cited by 26

The Subtle Trade-Off between Evolutionary and Energetic Constraints in Protein–Protein Interactions

Marchetti, F., Capelli, R., Rizzato, F., Laio, A., & Colombo, G. (2019) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.9b00191 · Cited by 26

Protein–Protein Interaction Interfaces and their Functional Implications

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Gastrodin ameliorates exercise-induced fatigue via modulating Nrf2 pathway and inhibiting inflammation in mice

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An automated microfluidic system for selection of aptamer probes against ovarian cancer tissues

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Protein–Protein Interaction Methods and Protein Phase Separation

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Network for network concept offers new insights into host- SARS-CoV-2 protein interactions and potential novel targets for developing antiviral drugs

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Different protein-protein interface patterns predicted by different machine learning methods

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