A Method for Detecting Overlapping Protein Complexes Based on an Adaptive Improved FCM Clustering Algorithm by Caixia Wang, Rongquan Wang, Kaiying Jiang

Subjects: “…protein–protein interaction network…”
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Non-enzymatic protein targeting agents as a promising strategy for cancer treatment by Madison Ambrose, Jeremy Lee, Aleem Syed, Zamal Ahmed, Guang Peng

Subjects: “…protein-protein interaction (PPI)…”
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Technologies for Proteome-Wide Discovery of Extracellular Host-Pathogen Interactions by Nadia Martinez-Martin

“…Nevertheless, the characterization of the proteins that function in the host-pathogen interface has been challenging, largely due to the technical challenges associated with detection of extracellular protein interactions. This review discusses available technologies for the high throughput study of extracellular protein interactions between pathogens and their hosts, with a focus on mammalian viruses and bacteria. …”
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Pupylation-based proximity labeling reveals regulatory factors in cellulose biosynthesis in Arabidopsis by Shuai Zheng, Lise C. Noack, Ouda Khammy, Andreas De Meyer, Ghazanfar Abbas Khan, Nancy De Winne, Dominique Eeckhout, Daniël Van Damme, Staffan Persson

“…Abstract Knowledge about how and where proteins interact provides a pillar for cell biology. Protein proximity-labeling has emerged as an important tool to detect protein interactions. …”
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Potential of Peptides as Inhibitors and Mimotopes: Selection of Carbohydrate-Mimetic Peptides from Phage Display Libraries by Teruhiko Matsubara

“…Inhibitors of carbohydrate-protein interactions are potential antiviral drugs. Several anti-influenza drugs such as oseltamivir and zanamivir are derivatives of sialic acid, which inhibits neuraminidase. …”
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Identification of cardiac premature senescence markers through GEO database interaction approach by Tiwuk Susantiningsih, Ani Retno Prijanti, Novi Silvia Hardiany, Fadilah

“…Conclusion: From the GeneCards, Cytoscape, and StringDB data, analysis of protein interactions in cardiac premature senescence showed that the protein-protein interactions with the highest scores were TP53, CDK2, and PTEN. …”
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Machine learning models for predicting interaction affinity energy between human serum proteins and hemodialysis membrane materials by Simin Nazari, Amira Abdelrasoul

“…Affinity energy, defined as the strength of interaction between membranes and human serum proteins, plays a crucial role in assessing membrane-protein interactions. These interactions may trigger adverse reactions, potentially harmful to patients. …”
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Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink by Lejla Gul, Anna Julia Elias, Tanvi Tambaku, Marton Olbei, Emily Watters, Balazs Bohar, Dezso Modos, Matthew Madgwick, Tamas Korcsmaros

“…Here, we present a protocol for predicting host-microbe protein-protein interactions and their downstream effects using MicrobioLink. …”
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The protein interactome of Escherichia coli carbohydrate metabolism. by Shomeek Chowdhury, Stephen S Fong, Peter Uetz

“…We investigate how protein-protein interactions (PPIs) can regulate carbohydrate metabolism in Escherichia coli. …”
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Integrative genomic analyses combined with molecular dynamics simulations reveal the impact of deleterious mutations of Bcl-2 gene on the apoptotic machinery and implications in ca... by Ghazi Elamin, Ghazi Elamin, Zhichao Zhang, Depika Dwarka, Kabange Kasumbwe, John Mellem, Nompumelelo P. Mkhwanazi, Paradise Madlala, Paradise Madlala, Mahmoud E. S. Soliman

“…Therefore, this study explores the association between SNPs in Bcl-2 and the structural, functional, protein-protein interactions (PPIs), drug binding and dynamic characteristics.MethodsComprehensive cross-validated bioinformatics tools and molecular dynamics (MD) simulations. …”
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The Roles of UmuD in Regulating Mutagenesis by Jaylene N. Ollivierre, Jing Fang, Penny J. Beuning

“…This paper focuses on the multiple conformations of the UmuD gene products and how their protein interactions regulate mutagenesis.…”
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Structural model of a bacterial focal adhesion complex by Christian Cambillau, Tâm Mignot

“…Despite understanding the system dynamics, its molecular structure and protein interactions remain unclear. In this study, we utilize AlphaFold to generate models based on the known interactions and dynamics of gliding motility proteins. …”
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Selecting Negative Samples for PPI Prediction Using Hierarchical Clustering Methodology by J. M. Urquiza, I. Rojas, H. Pomares, J. Herrera, J. P. Florido, O. Valenzuela

“…Protein-protein interactions (PPIs) play a crucial role in cellular processes. …”
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Unveiling the Molecular Architecture of HBV Spherical Subviral Particles: Structure, Symmetry, and Lipid Dynamics by Sonal Garg, Alyssa Ochetto, Jianming Hu, Joseph Che-Yen Wang

“…Recent advances in cryo-electron microscopy (cryo-EM) have uncovered the heterogeneity and dynamic nature of spherical HBV SVPs, emphasizing the essential role of lipid–protein interactions in maintaining particle stability. In this review, recent progress in understanding the molecular architecture of HBV SVPs is consolidated, focusing on their symmetry, lipid organization, and disassembly–reassembly dynamics. …”
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A comprehensive review of Interferometric Reflectance Imaging Sensor as a sensitive detection platform and its application areas by Monireh Bakhshpour-Yucel, Nese Lortlar Unlu, Elif Seymour, Adil Denizli

“…This review explores the underlying principles, instrumentation, and diverse applications of IRIS, with a focus on its efficacy for real-time monitoring of DNA-protein and protein-protein interactions, as well as virus detection. IRIS can measure DNA hybridization kinetics and identify pathogens without labeling, highlighting its versatility and reliability in biomedical research and diagnostics. …”
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The Effect of Highly Hydroxylated Fullerenol C60(OH)36 on Human Erythrocyte Membrane Organization by Jacek Grebowski, Anita Krokosz

“…The increase of the hw/hs parameter may be caused by changes in lipid-protein or protein-protein interactions which increase the mobility of the MSL label and as a result increase the membrane fluidity. …”
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Mechanism of Gene Amplification via Yeast Autonomously Replicating Sequences by Shelly Sehgal, Sanjana Kaul, M. K. Dhar

“…It was concluded that the mechanism of gene amplification was that AT rich tracts present in fragile sites of yeast serve as binding sites for MAR/SAR and DNA unwinding elements. The DNA protein interactions necessary for ORC activation are facilitated by DNA bending. …”
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Productive Entry Pathways of Human Rhinoviruses by Renate Fuchs, Dieter Blaas

“…Upon uptake into acidic compartments, the icosahedral HRV capsid expands by ~4% and holes open at the 2-fold axes, close to the pseudo-3-fold axes and at the base of the star-shaped dome protruding at the vertices. RNA-protein interactions are broken and new ones are established, the small internal myristoylated capsid protein VP4 is expelled, and amphipathic N-terminal sequences of VP1 become exposed. …”
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Crystal Structures of Tcl1 Family Oncoproteins and Their Conserved Surface Features by John M. Petock, Ivan Y. Torshin, Yuan-Fang Wang, Garrett C. Du Bois, Carlo M. Croce, Robert W. Harrison, Irene T. Weber

“…Analysis of the structures revealed conserved semi-planar surfaces that have characteristics of surfaces involved in protein-protein interactions. The Tcl1 proteins show differences in surface charge distribution and oligomeric state suggesting that they do not interact in the same way with Akt/PKB and other cellular protein(s).…”
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Targeting TLR/IL-1R Signalling in Human Diseases by Maria Loiarro, Vito Ruggiero, Claudio Sette

“…In particular, we will focus on inhibitors, such as decoy peptides and synthetic mimetics, that interfere with protein-protein interactions between signalling molecules of the TLR/IL-1R superfamily. …”
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