Network Pharmacology Analysis of the Therapeutic Potential of Colchicine in Acute Lung Injury by Fei Sun, Lijuan Zhang, Lulu Shen, Chunman Wang

“…We performed comprehensive pathway and process enrichment analyses on these genes. A protein-protein interaction network was constructed, and topological analysis was executed. …”
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Proteomic Characterization of Liver Cancer Cells Treated with Clinical Targeted Drugs for Hepatocellular Carcinoma by Hezhou Long, Jiafu Zhou, Changxia Zhou, Shuyu Xie, Jingling Wang, Minjia Tan, Junyu Xu

“…<b>Results</b>: Utilizing KEGG pathway enrichment analysis, biological process enrichment analysis, and protein interaction network analysis, we elucidated the common and specific metabolic pathways, biological processes, and protein interaction regulatory networks influenced by three liver cancer therapeutics. …”
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Identification and Validation of Pivotal Genes in Osteoarthritis Combined with WGCNA Analysis by Yang C, Chen X, Liu J, Wang W, Sun L, Xie Y, Chang Q

“…Functional enrichment analyses, protein-protein interaction (PPI) analysis, and weighted gene co-expression network analysis (WGCNA) of the DEGs were performed. …”
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Naoxintong Is Involved in the Coagulation Regulation of Warfarin Through the MAPK Pathway by Luo X, Chen L, Xu J, Li J

“…Cytoscape software was applied to construct the “drug-target”network; the protein interaction network (PPI) was used to study the protein-protein interaction. …”
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Transcriptome analysis of muscle atrophy in Leizhou black goats: identification of key genes and insights into limb-girdle muscular dystrophy by Ke Wang, Mengning Xu, Xiaotao Han, Hu Liu, Jiancheng Han, Wei Sun, Hanlin Zhou

“…Protein interaction network analysis identified five key clusters related to muscle function and development. …”
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Systematic analysis of co-expression network and gene expression profile of differentially expressed lncRNA-mRNA one week after spinal cord injury by Yi Kang, Yijie Song, Zhongju Shi, Qiang Li, Yigang Lv, Mengfan Hou, Cui Ding, Jing Xie, Yongfu Lou, Chi Zhang, Huan Jian, Xueying Li, Hengxing Zhou, Shiqing Feng

“…Moreover, we constructed protein–protein interaction (PPI) networks, the STRING database, and identified the 10 high degree core nodes. …”
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Interaction of the Wolbachia surface protein with a novel pro-viral protein from Aedes aegypti by Mazhar Hussain, Zhi Qi, Sassan Asgari

“…Here, we developed a hypothesis on whether Wolbachia proteins interact with pro-viral host proteins by using a unique approach to study the antiviral mechanism based on Wolbachia-host protein-protein interaction. …”
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Identification of biomarkers for chronic lymphocytic leukemia risk: a proteome-wide Mendelian randomization study by Changyu Jin, Zehong Lu, Yuzhan Chen, Huijie Hu, Miao Zhou, Yanli Zhang, Guifang Ouyang, Tongyu Li, Lixia Sheng

“…Additional analyses included colocalization, phenomenon-wide MR, and protein–protein interaction networks. Results The study identified nine plasma proteins significantly associated with CLL risk. …”
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Chemical Biology of G-quadruplex and i-motif DNA: use of topologically constrained DNA by Dejeu, Jérôme, Defrancq, Eric

“…., affine and specific) G4- and i-DNA-interacting ligands, (ii) identify proteins interacting with those structures and determine their cellular relevance and (iii) select specific antibodies for G4 and i-DNA. …”
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Dinuclear Copper(I) Thiodiacetate Complex-Mediated Expeditious Synthesis of the Chlorine-Containing Cyclen-Cored 36-Glucose-Coated Glycodendrimer by Anand K. Agrahari, Sunil Kumar, Anindra Sharma, Vinod K. Tiwari

“…High-sugar-tethered glycodendrimers are a remarkable tool in glycobiology for the investigation of carbohydrate-protein interaction using its multivalency property. An enthralling double-stage convergent synthetic approach was selected to build a novel class of chlorine-containing glucose-coated dendrimers using an efficient click catalyst ‘dinuclear copper(I) thiodiacetate complex.’ …”
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The Influence of Three Statistical Variables on Self-Similarity in Complex Networks by Mingli Lei, Lirong Liu, Daijun Wei

“…Moreover, two real networks are used for numerical simulation, including a USAir network and the yeast protein interaction (YPI) network. The effects of the three statistical variables on the two real networks are considered. …”
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LIN28A-dependent lncRNA NEAT1 aggravates sepsis-induced acute respiratory distress syndrome through destabilizing ACE2 mRNA by RNA methylation by Jun Liu, Xiang Li, Peng Yang, Yufeng He, Weilong Hong, Yawei Feng, Zhiqiang Ye

“…Methods Here RNA methylation was detected by methylated RNA immunoprecipitation (MeRIP), RNA stability was determined by RNA decay assay while RNA antisense purification (RAP) was used to identify RNA-protein interaction. Besides, co-immunoprecipitation (Co-IP) was utilized to detect protein-protein interaction. …”
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Molecular-genetic pathways of hepatitis C virus regulation of the expression of cellular factors PREB and PLA2G4C, which play an important role in virus replication by E. L. Mishchenko, A. A. Makarova, E. A. Antropova, A. S. Venzel, T. V. Ivanisenko, P. S. Demenkov, V. A. Ivanisenko

“…We assumed that NS3 could inhibit the function of host transcription factor (TF) NOTCH1 by protein-protein interaction, leading to upregulation of PREB and PLA2G4C. …”
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Structural information in therapeutic peptides: Emerging applications in biomedicine by Valentín Iglesias, Oriol Bárcenas, Carlos Pintado‐Grima, Michał Burdukiewicz, Salvador Ventura

“…This trend stems from their cost‐effectiveness and reduced immunogenicity, compared to antibodies or recombinant proteins, but also from their ability to dock and interfere with large protein–protein interaction surfaces, and their higher specificity and better biocompatibility relative to organic molecules. …”
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Exploring Drug Targets in Isoprenoid Biosynthetic Pathway for Plasmodium falciparum by Tabish Qidwai, Farrukh Jamal, Mohd Y. Khan, Bechan Sharma

“…For more comprehensive analysis, antimalarial drug-protein interaction has been covered.…”
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Structure‐based computational design of antibody mimetics: challenges and perspectives by Elton J. F. Chaves, Danilo F. Coêlho, Carlos H. B. Cruz, Emerson G. Moreira, Júlio C. M. Simões, Manassés J. Nascimento‐Filho, Roberto D. Lins

“…We discuss the intricacies of different computational protein–protein interaction design strategies, showcased by selected successful cases in the literature. …”
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CD163, a novel receptor for TNF, was revealed in situ by proximity ligation assay by Alexandre Cousin, Myriam Oger, Aymar de Jenlis, Audrey Lejart, Laure Barbier, Diane Riccobono, Xavier Holy, Anne-Laure Favier, Krisztina Nikovics

“…Our study compared co-localization using the Proximity Ligation Assay (PLA), a recently developed in situ protein-protein interaction technique. In an inflamed porcine lung model, we demonstrated the efficacy of PLA in detecting interactions between tumor necrosis factor (TNF) and its receptors TNFR1 and TNFR2. …”
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Identification of key miRNAs and target genes in extracellular vesicles derived from low-intensity pulsed ultrasound-treated stem cells by Xin Yin, Xin Yin, Jialian Yi, Fugang Mao, Qisheng Tang, Xinyu Zhang, Xiaoyu Yang, Hongqing Xie, Linping Wang, Shuifen Sun, Xin Yu, Xin Yu, Jie Liu, Lihong Jiang, Lihong Jiang

“…MiRNA-mRNA target analysis, functional and pathway enrichment analysis, protein-protein interaction network construction, and hub gene identification were conducted. …”
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Novel Clinical Insights into the Pathogenesis of Posttraumatic Elbow Stiffness: An Expression Profile Analysis of Contracted Joint Capsule in Human by Liu N, Dong J, Li L, Xu J, Yang C, Yu Z, Liu F

“…Functional enrichment analysis was performed, and the associated protein–protein interaction (PPI) network was constructed. MicroRNAs targeting these DEGs were identified, and transcription factors (TFs) targeting DEGs were predicted using the ENCODE database. …”
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Comparison of Protein Acetyltransferase Action of CRTAase with the Prototypes of HAT by Prija Ponnan, Ajit Kumar, Prabhjot Singh, Prachi Gupta, Rini Joshi, Marco Gaspari, Luciano Saso, Ashok K. Prasad, Ramesh C. Rastogi, Virinder S. Parmar, Hanumantharao G. Raj

“…The autoacetylation of CR like that of HATs was found to enhance protein-protein interaction. CR like HAT-1, CBP, and p300 mediated the acylation of RP utilizing acetyl CoA and propionyl CoA as the substrates. …”
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