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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Hypothesis generation for rare and undiagnosed diseases through clustering and classifying time-versioned biological ontologies. by Michael S Bradshaw, Connor Gibbs, Skylar Martin, Taylor Firman, Alisa Gaskell, Bailey Fosdick, Ryan Layer

“…Databases such as STRING contain millions of protein-protein interactions, and the Human Phenotype Ontology (HPO) contains the relations of thousands of phenotypes. …”
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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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Calcitonin/Amylin Receptors and Ramps by Patrick M. Sexton

“…Our understanding of G protein-coupled receptor function has recently expanded to encompass novel protein interactions that underlie both cell surface receptor expression and the exhibited phenotype. …”
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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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Mining functional gene modules by multi-view NMF of phenome-genome association by Xu Jin, WenQian He, MingMing Liu, Lin Wang, YaoGong Zhang, YingJie Xu, Ling Ma, YaLou Huang, MaoQiang Xie

“…CMNMF can also be a better tool for predicting members of gene pathways and protein-protein interactions.…”
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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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Exploring salivary gene expression clusters: A bioinformatics approach for advanced diagnosis and prognosis in head and neck squamous cell carcinoma by Rajesh Parsanathan, Rishaba Byju, D.S. Prabakaran

“…The aim is to identify critical genes and their protein-protein interactions through bio-computational analyses, contributing to a deeper understanding of HNSCC progression. …”
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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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A membrane permeability database for nonpeptidic macrocycles by Qiushi Feng, Danjo De Chavez, Jan Kihlberg, Vasanthanathan Poongavanam

“…Macrocycles show a particular ability to modulate difficult-to-drug targets, including protein-protein interactions, while still allowing oral administration. …”
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Protocol to identify endogenous proximal proteins using biotinylation by antibody recognition by Camilla Rega, Mercedes Pardo, Lesley-Ann Martin, Jyoti Choudhary

“…Summary: Biotinylation by antibody recognition (BAR) is an antibody-based approach for mapping proximal protein interactions in cells. Here, we present a protocol to biotinylate and identify proximal proteins using BAR. …”
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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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