Candidate Genes Associated with Delayed Neuropsychomotor Development and Seizures in a Patient with Ring Chromosome 20 by Thiago Corrêa, Amanda Cristina Venâncio, Marcial Francis Galera, Mariluce Riegel

“…Therefore, in this study, we can explore molecular cytogenetic data, identify proteins through network analysis of protein-protein interactions, and identify new candidate genes associated with the main clinical findings in patients with 20q13.33 deletions.…”
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Investigating the functional and structural effect of non-synonymous single nucleotide polymorphisms in the cytotoxic T-lymphocyte antigen-4 gene: An in-silico study. by Md Mostafa Kamal, Kazi Fahmida Haque Shantanu, Shamiha Tabassum Teeya, Md Motiar Rahman, A K M Munzurul Hasan, Douglas P Chivers, Tanveer A Wani, Atekah Hazzaa Alshammari, Mahesh Rachamalla, Francisco Carlos da Silva Junior, Md Munnaf Hossen

“…ConSurf predicted conservation scores for four nsSNPs, and Project Hope suggested that all mutations could disrupt protein interactions. Furthermore, mCSM and DynaMut2 analyses indicated a decrease in ΔΔG stability for the mutants. …”
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Computational and In silico study of novel fungicides against combating root rot, gray mold, fusarium wilt, and cereal rust. by Mollah Naimuzzaman, Md Mahabub Hasan, Ajoy Kumer, Abu Yousuf Hossin, Mohammad Harun-Ur-Rashid, Swapan Kumar Roy, Abu Noman Faruq Ahmmed, Jamal Uddin

“…Next, two docking tools, such as AutoDock by PyRx and Molecular Docking by Glide from the Schrödinger suite, were used to convey the docking score, and ligand protein interactions against four main proteases, for instance 7VEM, 8H6Q, 8EBB, and 7XDS having name of pathogens: Phytophthora capsici, Botrytis cinerea, Fusarium oxysporum f. sp. lycopersici, and Puccinia graminis f. sp. tritici, respectively. …”
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Acyl-CoA Thioesterase 1 Contributes to Transition of Steatosis to Metabolic-Associated Steatohepatitis by Elisa Pasini, Cristina Baciu, Marc Angeli, Bianca Arendt, Diogo Pellegrina, Jüri Reimand, Keyur Patel, George Tomlinson, Mohammad T. Mazhab-Jafari, Lakshmi P. Kotra, Sandra Fischer, Johane P. Allard, Atul Humar, Mamatha Bhat

“…Acyl-CoA thioesterase 1 (ACOT1) was identified as a critical node in the protein-protein interaction (PPI) network of the transition from steatosis to MASH in patient samples. …”
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Inherited Thrombocytopenia Related Genes: GPS2 Mediates the Interplay Between ANKRD26 and ETV6 by Valeria Capaci, Melania Eva Zanchetta, Giorgia Fontana, Daniele Ammeti, Roberta Bottega, Michela Faleschini, Anna Savoia

“…The <i>ANKRD26</i> gene, which encodes a protein involved in protein-protein interactions, is downregulated by RUNX1 during megakaryopoiesis. …”
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An Overview of the Intrinsic Role of Citrullination in Autoimmune Disorders by Mohammed Alghamdi, Doaa Alasmari, Amjad Assiri, Ehab Mattar, Abdullah A. Aljaddawi, Sana G. Alattas, Elrashdy M. Redwan

“…This modification leads to a charge shift, which affects the protein structure, protein-protein interactions, and hydrogen bond formation, and it may cause protein denaturation. …”
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Molecular characterization and functional annotation of a hypothetical protein (SCO0618) of A3(2) by Nadim Ferdous, Mahjerin Nasrin Reza, Md. Tabassum Hossain Emon, Md. Shariful Islam, A. K. M. Mohiuddin, Mohammad Uzzal Hossain

“…Furthermore, protein-protein interactions of selected hypothetical protein revealed several functional partners those have the significant role for the bacterial survival. …”
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Problems of creating antibody phage libraries and their solutions by V. S. Aripov, N. V. Volkova, A. A. Ilyichev, D. N. Shcherbakov

“…It has also become the basis for efficient and relatively inexpensive methods for studying protein–protein interactions, receptor binding sites, as well as epitope and mimotope identification. …”
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Elucidating the role of carrier proteins in cytokine stabilization within double emulsion‐based polymeric nanoparticles by Emily R. Rhodes, Nicole B. Day, Emma C. Aldrich, C. Wyatt Shields IV, Kayla G. Sprenger

“…We investigated protein–protein interactions between human (h)IL‐12 and albumin and simulated these components in pure water, dichloromethane (DCM), and along a water/DCM interface to replicate the solvent regimes formed during double emulsification. …”
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In Vitro Antibacterial, Antioxidant, Cytotoxicity Activity, and In Silico Molecular Modelling of Compounds Isolated from Roots of Hydnora johannis by Teshome Degfie, Milkyas Endale, Muhdin Aliye, Rajalakshmanan Eswaramoorthy, Tariku Nefo Duke, Aman Dekebo

“…Binding affinity scores of catechin (3)-protein interactions are in line with those from in vitro tests, indicating its potential antibacterial effect. …”
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A graph neural network approach for hierarchical mapping of breast cancer protein communities by Xiao Zhang, Qian Liu

“…Deep learning can automatically learn features from protein sequences and protein–protein interactions for hierarchical clustering. Results Using a large amount of publicly available proteomics data, we created a hierarchical tree for breast cancer protein communities using a novel hierarchical graph neural network, with the supervision of gene ontology terms and assistance of a pre-trained deep contextual language model. …”
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Comprehensive analysis of the prognostic, immunological, and diagnostic roles of SIRT1 in pan-cancer and its validation in KIRC by Qi Liu, Songxian Sun, Chunxiang Zhou, Houxi Xu, Houxi Xu

“…Various tools, including R, Cytoscape, HPA, Archs4, TISIDB, cBioPortal, STRING, GSCALite, and CancerSEA, were used to integrate and analyze SIRT1 gene expression, prognosis, protein interactions, signaling pathways, immune infiltration, and other relevant information. …”
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Four-color single-molecule imaging system for tracking GPCR dynamics with fluorescent HiBiT peptide by Toshiki Yoda, Yasushi Sako, Asuka Inoue, Masataka Yanagawa

“…Single-molecule imaging provides information on diffusion dynamics, oligomerization, and protein-protein interactions in living cells. To simultaneously monitor different types of proteins at the single-molecule level, orthogonal fluorescent labeling methods with different photostable dyes are required. …”
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MetArea: a software package for analysis of the mutually exclusive occurrence in pairs of motifs of transcription factor binding sites based on ChIP-seq data by V. G. Levitsky, A. V. Tsukanov, T. I. Merkulova

“…The multiprotein complex mapped in a ChIP-seq experiment includes target and other “partner” TFs linked by protein-protein interactions. Not all these TFs bind to DNA directly. …”
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Construction of Shoot Apical Meristem cDNA Yeast Library of <i>Brassica napus</i> L. and Screening of Proteins That Interact with the Inflorescence Regulatory Factors BnTFL1s by Lingxiong Zan, Haidong Liu, Xutao Zhao, Dezhi Du, Kaixiang Li

“…The recombination efficiency of the yeast two-hybrid (Y2H) library that we constructed was 100%, with insertion fragment lengths ranging from 750 to 2000 bp and a capacity of approximately 1.44 × 10⁷ CFUs (colony-forming units), sufficient for screening protein interactions. Additionally, the bait vector pGBKT7-BnTFL1s was transformed into yeast cells alongside positive and negative controls, demonstrating no toxicity to the yeast cells and no self-activation. …”
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In silico analysis of SNPs and miRNAs of KCTD13, CSDE1, SLC6A1 genes associated with autism spectrum disorder by Kübra Çoruh Kınalı, Ebru Özkan Oktay, Mesut Karahan

“…GeneMANIA and STRING were also employed to explore gene–gene and protein–protein interactions. Results A total of 16 variants in these three genes were estimated to be potentially harmful via in silico analysis. …”
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REVIEW ON PROTEIN FOOTPRINTING AS A TOOL IN STRUCTURAL BIOLOGY by Oluwatosin Ogundairo, Oluwatoyin Ayo-Farai, Chinedu Paschal Maduka, Chiamaka Chinaemelum Okongwu, Abdulraheem Olaide Babarinde, Olamide Sodamade

“…The application of protein footprinting in studying protein-protein interactions, ligand binding, and conformational changes is highlighted through a detailed examination of key studies and experimental approaches. …”
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Quantitative proteomic studies of the intestinal mucosa provide new insights into the molecular mechanism of ulcerative colitis by Yandong Guo, Dahal Pabitra, Lei Pan, Lanbo Gong, Aimin Li, Side Liu, Jing Xiong

“…Network analysis showed that proteins were involved in 4 pathways in UC-I and 3 pathways in UC-N tissues, and participated in protein-protein interactions. Increased expression of 9 DEPs, including TXNDC5, EPX, and ITGAM were detected in UC patients compared to normal control subjects. …”
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Phage display as a tool for identifying HIV-1 broadly neutralizing antibodies by A. N. Chikaev, A. P. Rudometov, Yu. A. Merkulyeva, L. I. Karpenko

“…Despite being a fairly old method, phage display is still widely used for studying protein-protein, peptide-protein and DNA-protein interactions due to its relative simplicity and versatility. …”
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Distinct subcellular localization of tau and alpha-synuclein in lewy body disease by D. Luke Fischer, Marissa Menard, Omar Z. Abdelaziz, Nicholas M. Kanaan, Virginia G. Cobbs, Richard E. Kennedy, Geidy E. Serrano, Thomas G. Beach, Laura A. Volpicelli-Daley

“…The relationship between tau and α-syn copathology is important for explaining clinical symptoms, severity, and progression, but there is no evidence for frequent, direct protein-protein interactions in the middle temporal gyrus.…”
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