State of the interactomes: an evaluation of molecular networks for generating biological insights by Sarah N Wright, Scott Colton, Leah V Schaffer, Rudolf T Pillich, Christopher Churas, Dexter Pratt, Trey Ideker

“…Here, we present a comprehensive evaluation of 45 current human interactomes, encompassing protein-protein interactions as well as gene regulatory, signaling, colocalization, and genetic interaction networks. …”
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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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Using Protein Painting Mass Spectrometry to Define Ligand Receptor Interaction Sites for Acetylcholine Binding Protein by Alexandru Graur, Natalie Erickson, Nadine Kabbani

“…We describe how the use of small molecule dyes can be optimized to uncover contact sites for ligand–protein interactions based on MS detection. Protein painting MS has been recently shown to be an effective tool for the identification of residues within Ac-AChBP involved in the binding of know ligands such as α-bungarotoxin. …”
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Familial Exudative Vitreoretinopathy-Related Disease-Causing Genes and Norrin/β-Catenin Signal Pathway: Structure, Function, and Mutation Spectrums by Hongtao Xiao, Yuna Tong, Yuxuan Zhu, Min Peng

“…Mutations have a tendency to cluster in some “hotspots” domains which may be responsible for protein interactions.…”
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A Cell Model for Conditional Profiling of Androgen-Receptor-Interacting Proteins by K. A. Mooslehner, J. D. Davies, I. A. Hughes

“…These preliminary results now allow future studies to focus on replacing wild-type AR with mutant AR to uncover differences in protein interactions caused by AR mutations involved in PAIS.…”
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Identifying Allosteric Small-Molecule Binding Sites of Inactive NS2B-NS3 Proteases of Pathogenic <i>Flaviviridae</i> by Hovakim Grabski, Siranuysh Grabska, Ruben Abagyan

“…The development of new therapeutic strategies based on inhibiting essential viral enzymes or viral–host protein interactions is problematic due to the fast mutation rate and rapid emergence of drug resistance. …”
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Escherichia coli O127 group 4 capsule proteins assemble at the outer membrane. by Matthew R Larson, Kassia Biddle, Adam Gorman, Sarah Boutom, Ilan Rosenshine, Mark A Saper

“…We identified a set of novel protein-protein interactions between GfcB, GfcC, and GfcD, both in vivo and in vitro, and quantified the binding properties with isothermal calorimetry and biolayer interferometry. …”
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In-Silico Evaluation of Binding Interaction and ADME Properties of Novel Pyrazoline and Pyrimidine Derivatives Targeting Cyclooxygenase-2 Enzyme by Sarmad Abbas Fadhil, Karima Fadhil Ali, Wesen Adel Mehde

“…Docking studies employing gold software facilitated the visualization of ligand-protein interactions, utilizing the crystal structure of the COX-2 protein (PDB ID: 4m11). …”
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A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages by Seung-Jin Park, Jong-Hwan Kim, Byung-Ha Yoon, Seon-Young Kim

“…Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. …”
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Continuous Delivery of D-Luciferin by Implanted Micro-osmotic Pumps Enables True Real-Time Bioluminescence Imaging of Luciferase Activity in Vivo by Shimon Gross, Ute Abraham, Julie L. Prior, Erik D. Herzog, David Piwnica-Worms

“…Bioluminescence imaging (BLI) of luciferase reporters in small animal models offers an attractive approach to monitor regulation of gene expression, signal transduction, and protein-protein interactions, as well as following tumor progression, cell engraftment, infectious pathogens, and target-specific drug action. …”
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WGCNA and integrative network analysis identify CHRNA5 and CTLA4 as potential therapeutic targets against angiosarcoma by Trishla Bhatnagar, Madiha Haider, Mohd Yasir Khan, Mohammad Zahid Ashraf

“…The intersection of true hub genes from MCC analysis of WGCNA modules and high-degree nodes from an unclustered network revealed eight consistently overexpressed genes in all angiosarcoma samples.Among the eight enriched genes, CHRNA5 and CTLA4, are exclusively overexpressed in angiosarcoma and not in other cancers of the same tissue origin, with significant drug-protein interactions suggesting their potential as therapeutic targets.…”
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Environmental and Genetic Variables Influencing Mitochondrial Health and Parkinson’s Disease Penetrance by Alessandra Zanon, Peter P. Pramstaller, Andrew A. Hicks, Irene Pichler

“…We discuss genetic and environmental factors as well as mitochondrial DNA alterations and protein-protein interactions, all involved in mitochondrial function, as potential causes to modify penetrance of mutations in dominant PD genes and to determine manifestation of heterozygous mutations in recessive PD genes.…”
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Emerging Role of Histone Acetyltransferase in Stem Cells and Cancer by Daniela Trisciuoglio, Marta Di Martile, Donatella Del Bufalo

“…Lysine acetylation can affect protein-nucleic acid or protein-protein interactions and protein localization, transport, stability, and activity. …”
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Unveiling the prognostic value of ARID3A in breast cancer through bioinformatic analysis by Wen-Run Cai, Xu-Gang Sun, Yue Yu, Xin Wang, Xu-Chen Cao, Xiao-Feng Liu

“…Functional enrichment analysis was conducted via LinkedOmics. Protein-protein interactions (PPI) were established using GeneMANIA and STRING, with validation through molecular docking using Cluspro. …”
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The role of BATF in immune cell differentiation and autoimmune diseases by Xiaomeng Wang, Yue Hong, Jinmei Zou, Bo Zhu, Chao Jiang, Liwei Lu, Jie Tian, Jing Yang, Ke Rui

“…Abstract As a member of the Activator Protein-1 (AP-1) transcription factor family, the Basic Leucine Zipper Transcription Factor (BATF) mediates multiple biological functions of immune cells through its involvement in protein interactions and binding to DNA. Recent studies have demonstrated that BATF not only plays pivotal roles in innate and adaptive immune responses but also acts as a crucial factor in the differentiation and function of various immune cells. …”
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Molecular docking reveals fibrinogen binding sites on SARS-CoV-2 spike protein: A potential mechanism for COVID-19-related coagulation by Onur Ozturk, Evren Kilinc, Batuhan Gorkem Irez, Emel Timucin

“…In this study, we investigated the protein-protein interactions between the SARS-CoV-2 spike protein and fibrinogen, a glycoprotein that plays a crucial role in blood coagulation. …”
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The E3 ubiquitin ligase MARCH1 mediates downregulation of plasma membrane GABAB receptors under ischemic conditions by inhibiting fast receptor recycling by Musadiq A. Bhat, Mohammad Hleihil, Irene Mondéjar, Thomas Grampp, Dietmar Benke

“…Recently, we developed interfering peptides targeting protein-protein interactions involved in downregulating the receptors. …”
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Genome-wide association studies are enriched for interacting genes by Peter T. Nguyen, Simon G. Coetzee, Irina Silacheva, Dennis J. Hazelett

“…The highest information objective function captured protein-protein interactions. We observed significantly greater fitness scores and subgraph sizes in foreground vs. matching sets of control variants. …”
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