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

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A "Silent" Polymorphism in the <i>MDR</i> 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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Why Do Hubs Tend to Be Essential in Protein Networks?

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Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?

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Folding funnels, binding funnels, and protein function

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Folding and binding cascades: Dynamic landscapes and population shifts

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Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes

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The molecular sociology of the cell

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Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms

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Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights

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Dynamic Complex Formation During the Yeast Cell Cycle

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

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Distributions of Exons and Introns in the Human Genome

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Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms

Tsai, C., del Sol, A., & Nussinov, R. (2009) · Molecular BioSystems · doi:10.1039/b819720b · Cited by 324 · see citing works

Evolvability and hierarchy in rewired bacterial gene networks

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End of the beginning

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Synonymous Mutations and Ribosome Stalling Can Lead to Altered Folding Pathways and Distinct Minima

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Combinatorial Control of Exon Recognition

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A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

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Structure of the Tfb1/p53 Complex: Insights into the Interaction between the p62/Tfb1 Subunit of TFIIH and the Activation Domain of p53

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How Do Proteins Interact?

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SnapShot: p53 Posttranslational Modifications

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Structural basis of Dscam isoform specificity

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Alternative Translation Initiation in Rat Brain Yields K2P2.1 Potassium Channels Permeable to Sodium

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

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Emerging roles of BRCA1 alternative splicing

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Creative elements: network-based predictions of active centres in proteins and cellular and social networks

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Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins

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Protein–protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach

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Toward accurate reconstruction of functional protein networks

Yosef, N., Ungar, L., Zalckvar, E., Kimchi, A., Kupiec, M., Ruppin, E., & Sharan, R. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.3 · Cited by 91 · see citing works

Variations in Clique and Community Patterns in Protein Structures during Allosteric Communication: Investigation of Dynamically Equilibrated Structures of Methionyl tRNA Synthetase Complexes

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p38α and p38γ Mediate Oncogenic ras-induced Senescence through Differential Mechanisms

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Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example

Tunçbağ, N., Kar, G., Gürsoy, A., Keskin, Ö., & Nussinov, R. (2009) · Molecular BioSystems · doi:10.1039/b905661k · Cited by 78 · see citing works

How Perfect Can Protein Interactomes Be?

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p53 isoforms - A conspiracy to kidnap p53 tumor suppressor activity?

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Alternative splicing in human transcriptome: Functional and structural influence on proteins

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Control of the single channel conductance of K2P10.1 (TREK‐2) by the amino‐terminus: role of alternative translation initiation

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Conformational Switching upon Phosphorylation: A Predictive Framework Based on Energy Landscape Principles

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Drug-therapy networks and the prediction of novel drug targets

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Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions

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Towards Drugs Targeting Multiple Proteins in a Systems Biology Approach

Keskin, Ö., Gürsoy, A., Ma, B., & Nussinov, R. (2007) · Current Topics in Medicinal Chemistry · doi:10.2174/156802607780906690 · Cited by 51 · see citing works

Molecular diversity of Dscam: recognition of molecular identity in neuronal wiring

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Molecular and in silico analysis of BRCA1 and BRCA2 variants

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Functional characterization of p53β and p53γ, two isoforms of the tumor suppressor p53

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Energetic determinants of protein binding specificity: Insights into protein interaction networks

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Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes

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Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis

Tozluoǧlu, M., Karaca, E., Haliloǧlu, T., & Nussinov, R. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn481 · Cited by 26 · see citing works

Alternative translation initiation further increases the molecular and functional diversity of ion channels

Honoré, É. (2008) · The Journal of Physiology · doi:10.1113/jphysiol.2008.165019 · Cited by 8 · see citing works

Refocusing on BRCA1

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Structure and dynamics of molecular networks: A novel paradigm of drug discovery

Csermely, P., Korcsmáros, T., Kiss, H., London, G., & Nussinov, R. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.01.016 · Cited by 889 · see citing works

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436 · see citing works

iLoc-Hum: using the accumulation-label scale to predict subcellular locations of human proteins with both single and multiple sites

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Nonspecific Binding—Fundamental Concepts and Consequences for Biosensing Applications

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The Ribosome as a Hub for Protein Quality Control

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Protein binding specificity versus promiscuity

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Allosteric post-translational modification codes

Nussinov, R., Tsai, C.-J., Xin, F., & Radivojac, P. (2012) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2012.07.001 · Cited by 211 · see citing works

Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks

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Expanding the proteome: disordered and alternatively folded proteins

Dyson, H. J. (2011) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583511000060 · Cited by 173 · see citing works

The Underappreciated Role of Allostery in the Cellular Network

Nussinov, R., Tsai, C., & Ma, B. (2013) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-083012-130257 · Cited by 174 · see citing works

Hub Promiscuity in Protein-Protein Interaction Networks

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Rational Design of Peptide-Based Inhibitors Disrupting Protein-Protein Interactions

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Cross talk between stimulated NF-κB and the tumor suppressor p53

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Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

Nussinov, R., Jang, H., Tsai, C., & Cheng, F. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006658 · Cited by 129 · see citing works

New Force Field on Modeling Intrinsically Disordered Proteins

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Quantitative proteomics in lung cancer

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Targeting Intrinsically Disordered Transcription Factors: Changing the Paradigm

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Topology of molecular interaction networks

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Protein ensembles link genotype to phenotype

Nussinov, R., Tsai, C., & Jang, H. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006648 · Cited by 98 · see citing works

Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs

Vandereyken, K., Leene, J. V., Coninck, B. D., & Cammue, B. P. A. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.00694 · Cited by 98 · see citing works

PTEN proteoforms in biology and disease

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ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins

Song, D., Wang, W., Ye, W., Ji, D., Luo, R., & Chen, H. (2016) · Chemical Biology & Drug Design · doi:10.1111/cbdd.12832 · Cited by 85 · see citing works

Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins

Ye, W., Ji, D., Wang, W., Luo, R., & Chen, H. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5b00043 · Cited by 80 · see citing works

Local and global anatomy of antibody‐protein antigen recognition

Wang, M., Zhu, D. S., Zhu, J., Nussinov, R., & Ma, B. (2017) · Journal of Molecular Recognition · doi:10.1002/jmr.2693 · Cited by 76 · see citing works

Antigen binding allosterically promotes Fc receptor recognition

Zhao, J., Nussinov, R., & Ma, B. (2018) · mAbs · doi:10.1080/19420862.2018.1522178 · Cited by 79 · see citing works

Ferroptosis – An iron- and disorder-dependent programmed cell death

Djulbegovic, M. B., & Uversky, V. N. (2019) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2019.05.221 · Cited by 77 · see citing works

Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions

Cukuroglu, E., Gürsoy, A., Nussinov, R., & Keskin, Ö. (2014) · PLoS ONE · doi:10.1371/journal.pone.0086738 · Cited by 76 · see citing works

Disparate Degrees of Hypervariable Loop Flexibility Control T-Cell Receptor Cross-Reactivity, Specificity, and Binding Mechanism

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A Novel Co-immunoprecipitation Protocol Based on Protoplast Transient Gene Expression for Studying Protein–protein Interactions in Rice

Yang, J., Fu, J. X., Li, J., Cheng, X. L., Feng, L., Dong, J. F., Liu, Z. L., & Zhuang, C. X. (2013) · Plant Molecular Biology Reporter · doi:10.1007/s11105-013-0633-9 · Cited by 76 · see citing works

One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade

Villoutreix, B. O., Lagorce, D., Labbé, C. M., Spérandio, O., & Miteva, M. A. (2013) · Drug Discovery Today · doi:10.1016/j.drudis.2013.06.013 · Cited by 72 · see citing works

MultitaskProtDB: a database of multitasking proteins

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An overview of recent advances in structural bioinformatics of protein–protein interactions and a guide to their principles

Sudha, G., Nussinov, R., & Srinivasan, N. (2014) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2014.07.004 · Cited by 69 · see citing works

Scale invariance in natural and artificial collective systems: a review

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Pathogen mimicry of host protein-protein interfaces modulates immunity

Guven‐Maiorov, E., Tsai, C., & Nussinov, R. (2016) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2016.06.004 · Cited by 68 · see citing works

AptaNet as a deep learning approach for aptamer–protein interaction prediction

Emami, N., & Ferdousi, R. (2021) · Scientific Reports · doi:10.1038/s41598-021-85629-0 · Cited by 68 · see citing works

Constructing structural networks of signaling pathways on the proteome scale

Kuzu, G., Keskin, Ö., Gürsoy, A., & Nussinov, R. (2012) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.04.004 · Cited by 64 · see citing works

Established and Emerging Trends in Computational Drug Discovery in the Structural Genomics Era

Taboureau, O., Baell, J. B., Fernández‐Recio, J., & Villoutreix, B. O. (2012) · Chemistry & Biology · doi:10.1016/j.chembiol.2011.12.007 · Cited by 63 · see citing works

Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation

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Cell growth and cell cycle in Saccharomyces cerevisiae: Basic regulatory design and protein–protein interaction network

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Domain distribution and intrinsic disorder in hubs in the human protein–protein interaction network

Patil, A., Kinoshita, K., & Nakamura, H. (2010) · Protein Science · doi:10.1002/pro.425 · Cited by 62 · see citing works

Allosteric Conformational Barcodes Direct Signaling in the Cell

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How yeast can be used as a genetic platform to explore virus–host interactions: from ‘omics’ to functional studies

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The spatial structure of cell signaling systems

Nussinov, R. (2013) · Physical Biology · doi:10.1088/1478-3975/10/4/045004 · Cited by 49 · see citing works

Multispecific Recognition: Mechanism, Evolution, and Design

Erijman, A., Aizner, Y., & Shifman, J. M. (2011) · Biochemistry · doi:10.1021/bi101563v · Cited by 47 · see citing works

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions

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Analysis of Hot Region Organization in Hub Proteins

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

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