Protein–protein interaction networks: how can a hub protein bind so many different partners?

Emergence of Scaling in Random Networks

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Finishing the euchromatic sequence of the human genome

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Functional organization of the yeast proteome by systematic analysis of protein complexes

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A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

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Network pharmacology: the next paradigm in drug discovery

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Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

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A "Silent" Polymorphism in the MDR 1 Gene Changes Substrate Specificity

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Evidence for dynamically organized modularity in the yeast protein–protein interaction network

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Flexible nets: The roles of intrinsic disorder in protein interaction networks

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Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

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KCC2 is a hub protein that balances excitation and inhibition

Pressey, J. C., Mahadevan, V., & Woodin, M. A. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-815318-5.00008-x · Cited by 6

A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions

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Design in biology and rational design in vaccinology: A conceptual analysis

Regenmortel, M. H. V. V. (2021) · Methods · doi:10.1016/j.ymeth.2021.07.010 · Cited by 5

Prospects of Modulating Protein–Protein Interactions

Zhong, S., Oashi, T., Yu, W., Shapiro, P., & MacKerell, A. D. (2012) · Wiley eBooks · doi:10.1002/9783527645947.ch15 · Cited by 5

CDH1 overexpression sensitizes TRAIL resistant breast cancer cells towards rhTRAIL induced apoptosis

Tapadar, P., Pal, A., Ghosal, N., Kumar, B., Paul, T., Biswas, N., & Pal, R. (2023) · Molecular Biology Reports · doi:10.1007/s11033-023-08657-1 · Cited by 4

Arginine (315) is required for the PLIN2-CGI-58 interface and plays a functional role in regulating nascent LDs formation in bovine adipocytes

Li, P., Mei, C., Raza, S. H. A., Cheng, G., Ning, Y., Zhang, L., & Zan, L. (2024) · Genomics · doi:10.1016/j.ygeno.2024.110817 · Cited by 4

Topological, functional, and structural analyses of protein-protein interaction networks of breast cancer lung and brain metastases

Halakou, F., Gürsoy, A., Sen-Kilic, E., & Keskin, Ö. (2017) · IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) · doi:10.1109/cibcb.2017.8058539 · Cited by 4

HormoNet: a deep learning approach for hormone-drug interaction prediction

Emami, N., & Ferdousi, R. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05708-7 · Cited by 3

Structure Collisions between Interacting Proteins

Emig, D., Sander, O., Mayr, G., & Albrecht, M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019581 · Cited by 3

Characterization and Evolutionary Analysis of Protein–Protein Interaction Networks

Musso, G. A., Emili, A., & Zhang, Z. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-585-5_15 · Cited by 3

Construction and Analysis of Protein-Protein Interaction Network

Dasagrandhi, D., Ravindran, A. S. K., Anusuyadevi, M., & S., J. K. (2018) · Advances in medical technologies and clinical practice book series · doi:10.4018/978-1-5225-7326-5.ch009 · Cited by 3

Simulation of biochemical systems using constraint-based methods and complex networks

Burke, P. E. P. (2021) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.95.2021.tde-23032021-143111 · Cited by 2

Target Mapping in Cancer: Ligandable Protein Pockets on 3D OncoPPI Networks

Trisciuzzi, D., Nicolotti, O., Cruciani, G., Menna, G., & Siragusa, L. (2025) · Pharmaceuticals · doi:10.3390/ph18070958 · Cited by 2

Evaluating global measures of network centralization: Axiomatic and numerical assessments

Saberi, M., & Aref, S. (2026) · PLoS ONE · doi:10.1371/journal.pone.0341630 · Cited by 2

Network pharmacology and molecular docking-based insights into the anti-melanoma potential of dalbergin

Vijh, D., Singh, A., Mansi, Khanna, L., & Gupta, P. (2026) · In Silico Pharmacology · doi:10.1007/s40203-026-00604-9 · Cited by 2

Molecular Biomarker Identification Using a Network-Based Bioinformatics Approach That Links COVID-19 With Smoking

Rahman, M. A., Amin, M. A., Yeasmin, M. N., & Islam, M. Z. (2023) · Bioinformatics and Biology Insights · doi:10.1177/11779322231186481 · Cited by 2

Gaussian Beltrami-Klein Model for Protein Sequence Classification: A Hyperbolic Approach

Ali, S., Mansoor, H., Chourasia, P., Ali, Y., & Patterson, M. (2024) · Lecture notes in computer science · doi:10.1007/978-981-97-5128-0_5 · Cited by 2

Mechanism of salvianolic acid B treating coronary artery disease based on dynamic network modules

Huo, M., Zhang, Y., ZHENG, S., & Qiao, Y. (2016) · Scientia Sinica Vitae · doi:10.1360/n052016-00020 · Cited by 2

The roles of contact residue disorder and domain composition in characterizing protein–ligand binding specificity and promiscuity

Tang, Y., Sheng, X., & Stumpf, M. P. H. (2011) · Molecular BioSystems · doi:10.1039/c1mb05325f · Cited by 1

Preserving Hidden Hierarchical Structure: Poincaré Distance for Enhanced Genomic Sequence Analysis

Ali, S., Mansoor, H., Chourasia, P., Khan, I. U., & Patterson, M. (2025) · Communications in computer and information science · doi:10.1007/978-3-031-91428-7_1 · Cited by 1

Drug Discovery by Targeting Protein–Protein Interactions

Bettinetti, L., Magnani, M., & Padova, A. (2013) · Springer eBooks · doi:10.1007/978-3-642-37999-4_1 · Cited by 1

Energy landscape investigation by wavelet transform analysis of atomic force spectroscopy data in a biorecognition experiment

Bizzarri, A. R. (2015) · Journal of Biological Physics · doi:10.1007/s10867-015-9398-8 · Cited by 1

Identifying Hub Proteins and Their Essentiality from Protein-protein Interaction Network

Bakar, S. A., Taheri, J., & Zomaya, A. Y. (2011) · IEEE International Conference on Bioinformatics and Bioengineering (BIBE) · doi:10.1109/bibe.2011.67 · Cited by 1

Low-Level Laser Therapy Effects on Rat Blood Hemostasis Via Significant Alteration in Fibrinogen and Plasminogen Expression Level

Arjmand, B., Khodadost, M., Sherafat, S. J., Rezaei–Tavirani, M., Ahmadi, N., Okhovatian, F., & Tavirani, M. R. (2021) · Journal of lasers in medical sciences · doi:10.34172/jlms.2021.59 · Cited by 1

Caracterização dos aminoácidos da interface proteína-proteína com maior contribuição na energia de ligação e sua predição a partir dos dados estruturais

Pereira, J. G. D. C. (2012) · doi:10.47749/t/unicamp.2012.901414 · Cited by 1

WITHDRAWN: A Temporal Atlas of the Nuclear Androgen Receptor Proximal InteractomePreprint

Ptak, C. C., Eng, J. K., Radoshevich, L., & Wright, M. E. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.03.742470 · Cited by 1

Structural and functional interrogation of Anterior Gradient-2

Gray, T. A. (2013) · ERA

Systems Pharmacology and Pharmacogenomics for Drug Discovery and Development

Talwar, P., Silla, Y., Grover, S., Gupta, M., Grewal, G. K., & Kukreti, R. (2014) · Springer eBooks · doi:10.1007/978-94-017-9514-2_9

Structural insights into Arginine-Serine rich proteins and N-H spin-spin coupling constants

Xiang, S. (2013) · doi:10.53846/goediss-4157

RNA Processing, Translational Regulation, and RNA Interference

Krauss, G. (2014) · doi:10.1002/9783527667475.ch05

Structural Properties, Regulation and Posttranslational Modification of Signaling Proteins

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Viral Species, Viral Genomes and HIV Vaccine Design: Is the Rational Design of Biological Complexity a Utopia?

Regenmortel, M. H. V. V. (2019) · Springer eBooks · doi:10.1007/978-3-030-32459-9_24

Integration of Gastric Cancer RNA ‐Seq Datasets Along With PPI Network Suggests That Nonhub Nodes Have the Potential to Become Biomarkers

Siavoshi, A., Piran, M., Sharifi‐Zarchi, A., & Ataellahi, F. (2025) · Cancer Reports · doi:10.1002/cnr2.70126

Next-Generation Computational Approaches for Biological Network Analysis

Mari, H. A., Taqi, M., Rattar, A. A., Memon, A. J., Nasir, M. T., & Yousuf, A. (2025) · BioMed Target Journal · doi:10.59786/bmtj.313

A tethering mechanism underlies Pin1-catalyzed proline cis–trans isomerization at a noncanonical site

Williams, C. C., Chuck, J., Munoz‐Tello, P., & Kojetin, D. J. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2414606122

Kinetic and Conformational Characterization of Transcriptional Activator-Coactivator Interactions.

Wang, N. (2013) · Deep Blue (University of Michigan)

Additional file 3 of HormoNet: a deep learning approach for hormone-drug interaction prediction

Emami, N., & Ferdousi, R. (2024) · Figshare · doi:10.6084/m9.figshare.26686791

Additional file 2 of HormoNet: a deep learning approach for hormone-drug interaction prediction

Emami, N., & Ferdousi, R. (2024) · Figshare · doi:10.6084/m9.figshare.26686788

Additional file 1 of HormoNet: a deep learning approach for hormone-drug interaction prediction

Emami, N., & Ferdousi, R. (2024) · Figshare · doi:10.6084/m9.figshare.26686785

Development of a global screening system for detecting protein–protein interactions by luminescence complementation in fission yeast

Azadeh, F., Hashimoto, A., Nishimura, S., Arioka, M., Yoshida, M., & Matsuyama, A. (2026) · Scientific Reports · doi:10.1038/s41598-026-35430-8

Synthetic Microbial Communities—A New Frontier in Plant Microbiology

Acharya, A., Jurgenson, C. T., Shanmugam, S. G., Norton, A., & Oelke, M. (2026) · Applied Microbiology · doi:10.3390/applmicrobiol6090100

Hub Promiscuity in Protein-Protein Interaction Networks

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Structural properties of hub proteins

Cukuroglu, E., Özkırımlı, E., & Keskin, Ö. (2010) · International Symposium on Health Informatics and Bioinformatics (HIBIT) · doi:10.1109/hibit.2010.5478881 · Cited by 2

Similar Binding Sites and Different Partners: Implications to Shared Proteins in Cellular Pathways

Keskin, O., & Nussinov, R. (2007) · Structure · doi:10.1016/j.str.2007.01.007 · Cited by 144

The Role Of Dynamics On Binding Specificity And Promiscuity

Özkırımlı, E., & Keskin, Ö. (2009) · Biophysical Journal · doi:10.1016/j.bpj.2008.12.2275

What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?

Ekman, D. S., Light, S., Björklund, Å. K., & Elofsson, A. (2006) · Genome biology · doi:10.1186/gb-2006-7-6-r45 · Cited by 378