Deep learning–based assessment of missense variants in the COG4 gene presented with bilateral congenital cataract by Shaohua Zhang, Yang Sun, Yinghong Ji, Li Ning, Binghe Xiao, Maierdanjiang Ainiwaer, Houyi Liu, Yingying Hong

“…Objective We compared the protein structure and pathogenicity of clinically relevant variants of the COG4 gene with AlphaFold2 (AF2), Alpha Missense (AM), and ThermoMPNN for the first time.Methods and analysis The sequences of clinically relevant Cog4 missense variants (one novel identified p.Y714F and three pre-existing p.G512R, p.R729W and p.L769R from Uniprot Q9H9E3) were imported into AF2 for protein structural prediction, and the pathogenicity was estimated using AM and ThermoMPNN. …”
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The Campylobacter jejuni BumS sensor phosphatase detects the branched short-chain fatty acids isobutyrate and isovalerate as direct cues for signal transduction by Nestor Ruiz, Jiawei Xing, Igor B. Zhulin, Chad A. Brautigam, David R. Hendrixson

“…Isobutyrate and isovalerate reduced the thermostability of BumS and caused a reorganization of protein structure to suggest how sensing these cues inhibits phosphatase activity. …”
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The role of flavonoids in mitigating food originated heterocyclic aromatic amines that concerns human wellness by Hui Teng, Hongting Deng, Chang Zhang, Hui Cao, Qun Huang, Lei Chen

“…However, heating processes cause the meat to become more appetizing with changes in texture, appearance, flavor, and chemical properties by the altering of protein structure and other ingredients. As one kind of cooking-induced contaminants, heterocyclic aromatic amines (HAAs) are widely present in protein aceous food products with strong carcinogenic and mutagenic properties. …”
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In silico evaluation of missense SNPs in cancer-associated Cystatin A protein and their potential to disrupt Cathepsin B interaction by Shafaat Hossain, Omar Hamza Bin Manjur, Mst Sharmin Sultana Shimu, Tamanna Sultana, Mustafizur Rahman Naim, Shahariar Siddique, Abdullah Al Mamun, Md Miftaur Rahman, Md Abu Saleh, Md Rakibul Hasan, Tania Rahman

“…These findings suggest that the E94K mutation could affect the protein structure and cathepsin B interaction, potentially leading to pathological consequences as evidenced by colorectal adenocarcinoma patients in the COSMIC (Catalogue of Somatic Mutations in Cancer) database.…”
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Modification of hempseed protein isolate using a novel two-stage method applying high-pressure homogenization coupled with high-intensity ultrasound by Ruyu Zhang, Wangang Zhang, Xuan Dong, Meng Wai Woo, Siew Young Quek

“…This treatment significantly decreased the HPI’s particle size, β-sheet and total sulfhydryl contents while maximizing the random coil level, intrinsic fluorescence intensity and surface hydrophobicity compared to the single HPH or HIU2min treatments. The protein structure was modified and unfolded, enhancing the water-protein and oil-protein interactions, as reflected in the increase in water and oil absorption, foaming and emulsifying properties. …”
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Mapping knowledge landscapes and emerging trends in artificial intelligence for antimicrobial resistance: bibliometric and visualization analysis by Zhongli Wang, Zhongli Wang, Gaopei Zhu, Shixue Li, Shixue Li

“…Citation analysis highlighted two major breakthroughs: AlphaFold’s protein structure prediction (6,811 citations) and deep learning approaches to antibiotic discovery (4,784 citations). …”
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Molecular Characterization and Evolution Analysis of Two Forms of TLR5 and TLR13 Genes Base on Larimichthys crocea Genome Data by Lihua Jiang, Liyi Pei, Ping Wang, Liqin Liu, Gong Li, Binjian Liu, Zhenming Lǚ, Tabata Hiromasa, Hao Pan, Atsushi Ogura

“…Here, the full-length coding sequence (CDS), protein structure, and immune response and subcellular localization of TLR5 (TLR5S) and TLR13 were characterized in large yellow croaker (Larimichthys crocea). …”
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Identification of core genes related to exosomes and screening of potential targets in periodontitis using transcriptome profiling at the single-cell level by Wufanbieke Baheti, Diwen Dong, Congcong Li, Xiaotao Chen

“…GSEA revealed that ribosome was co-enriched by 5 core genes, manifesting the expression of these genes might be critical for protein structure or function. Immunoinfiltration analysis found that CKAP2, IGLL5, MZB1, and CXCL6 exhibited positive correlations with most discrepant immune cells/discrepant stromal cells, which were highly infiltrated in PD. …”
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Association between ABCB4 variants and intrahepatic cholestasis of pregnancy by Dekun Zhang, Yuhong Li, Shufeng He, Jing Shu, Tiechen Li, Qing Sun

“…PolyPhen2, Mutation Taster, Provean, SIFT and Mutpred2 were used to predict protein structure, and Pymol software was used to predict the impact of missense variant c.1954 A > G(p.Arg652Gly) on proteins. …”
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Construction and high-throughput screening of gradient nanowire coatings on titanium surface towards ameliorated osseointegration by Ruiyue Hang, Yuyu Zhao, Huanming Chen, Xiaomei Li, Runhua Yao, Yonghua Sun, Xiaohong Yao, Long Bai, Huaiyu Wang, Yong Han, Ruiqiang Hang

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Integration of ATAC-seq and RNA-seq reveals signal regulation during post-molt and inter-molt stages in muscle of Eriocheir sinensis by Bin Wang, Bin Wang, Jingjing Li, Mingzhi Zhang, Mingzhi Zhang, Anqi Li, Zhentao Song, Zhentao Song, Zhen He, Zhen He, Ruiqi Zhang, Ruiqi Zhang, Tong Hao, Tong Hao, Jinsheng Sun, Jinsheng Sun

“…In all the enriched signaling pathways, GPCR signaling pathway includes the most differentially expressed genes (8 genes), which underlines its importance in the signal transduction from the post-molt stage to the inter-molt stage. Further protein structure analysis and RT-qPCR validation confirmed five GPCR genes related to molting process, in which four genes (GRM7, FMRFaR, mth2, gpr161) are active during the post-molt stage and one gene (moody) functions during the inter-molt stage.DiscussionThese findings highlight the key regulatory proteins and pathways involved in E. sinensis muscle during molting and also offer foundational data for studying the mechanisms of molting and discontinuous growth in crustaceans.…”
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A rare deleterious missense mutation in the AXIN2 gene in Chinese women with polycystic ovary syndrome by Ying Zhang, Yu Chen, Fa-Ying Liu, Jing-Wen Fu, Xian-Xian Liu, Jun Tan, Ou-Ping Huang, Yang Zou

“…The evolutionary conservation analysis of the identified Axin-2 mutant was analyzed among 15 vertebrates from human to zebrafish. The protein structure change was analyzed between the wild-type and mutation-type. …”
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Tat-fimbriae (“tafi”): An unusual type of haloarchaeal surface structure depending on the twin-arginine translocation pathway by Anna V. Galeva, Dahe Zhao, Alexey S. Syutkin, Marina Yu Topilina, Sergei Yu Shchyogolev, Elena Yu Pavlova, Olga M. Selivanova, Igor I. Kireev, Alexey K. Surin, Gennady L. Burygin, Jingfang Liu, Hua Xiang, Mikhail G. Pyatibratov

“…Molecular genetic evidence demonstrates TafA was transported through the twin-arginine translocation pathway (Tat-pathway). Based on protein structure prediction (including AlphaFold 3), tafi exhibits a linear structure: TafC at the tip, TafE acting as an adapter, TafA forming the core filament, and they link the fourth subunit TafF, anchoring tafi to the cell wall. …”
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From structure prediction to function: defining the domain on the African swine fever virus CD2v protein required for binding to erythrocytes by Ana Luisa Reis, Anusyah Rathakrishnan, Vlad Petrovan, Muneeb Islam, Lynnette Goatley, Katy Moffat, Mai Tuyet Vuong, Yuan Lui, Simon J. Davis, Shinji Ikemizu, Linda K. Dixon

“…A combination of protein structure modeling and extensive mutagenesis was used to identify residues mediating binding of transiently expressed CD2v to erythrocytes. …”
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Deciphering the role of flutamide, fluorouracil, and furomollugin based ionic liquids in potent anticancer agents: Quantum chemical, medicinal, molecular docking and MD simulation... by Danish Ali, Muhammad Arif Ali, Muhammad Sarfraz, Afifa Yousuf, Rasham Zulfiqar, Abdul Rauf, Hong-Liang Xu, Muhammad Arshad

“…In addition, Ramachandran plots indicate that >90 % of residues occupy the favored regions supporting the protein structure stability. Thus, these analyses confirm that the newly identified ILs exhibit superior binding affinities and acceptable bioinformatics profiles, making them attractive candidates for the development of anticancer drugs.…”
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Application of copy number variation sequencing combined with whole exome sequencing in prenatal left–right asymmetry disorders by Yu Qin, Muon Senglong, Koksear Touch, Juan Xiao, Ruijie Fang, Qingling kang, Lei Fan, Shufang Li, Jing Liu, Jianli Wu, Yuanyuan Wu, Xinwei Shi, Haiyi Liu, Xun Gong, Xingguang Lin, Ling Feng, Suhua Chen, Wei Li

“…Further bioinformatics scrutiny was conducted to assess the protein structure and function prediction of these variants, ultimately indicating their potential pathogenicity. …”
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Cucumeropsis mannii seed oil shields against cyclophosphamide-induced hepatorenal toxicity by modulating redox imbalance and iNOS/IL-β1 signalling in rats by Amaka Cecilia Agbara, Ejike Daniel Eze, Christian Emeka Offor, Adam Moyosore Afodun, Ezebuilo Ugbala Ekpono, Peter Chinedu Agu, Chinyere Aloke, Nkeiru Nwaamaka Ezeani, Emmanuel Orire Ikuomola, Ekom Monday Etukudo, Ilemobayo Victor Fasogbon, Angela Mumbua Musyoka, Patrick Maduabuchi Aja

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Association study of the JAK/STAT signaling pathway with susceptibility to COVID-19 in moroccan patient and in-silico analysis of rare variants by Meriem El Houdi, Hanaa Skhoun, Meriem El Fessikh, Reda Benmansour, Fatima-Zahra El Yousfi, Chaimae Nebhani, Mohamed Rida Tagajdid, Idriss Lahlou Amine, Hicham El Annaz, Rabii Ameziane El Hassani, Zohra Ouzzif, Redouane Abouqal, Khalid Ennibi, Ahmed Bouhouche, Jamila El Baghdadi

“…Notably, IFNAR1 p.Val168Leu mutated C allele was significantly associated with reduced susceptibility to COVID-19 severity (p=0.028, OR=0.5936 [0.3725 – 0.9461]), under the additive model (p=0.045, OR=0.626 [0.3958 – 0.9899]).Rare variants IFNAR1 p.Trp318Cys, p.Ser476Phe, and IFNAR2 p.Cys271Tyr were predicted deleterious, impacting protein structure via hydrogen bond and hydrophobic interaction alterations. …”
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DPFunc: accurately predicting protein function via deep learning with domain-guided structure information by Wenkang Wang, Yunyan Shuai, Min Zeng, Wei Fan, Min Li

“…DPFunc can detect significant regions in protein structures and accurately predict corresponding functions under the guidance of domain information. …”
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Bioinformatics analysis of myelin-microbe interactions suggests multiple types of molecular mimicry in the pathogenesis of multiple sclerosis. by Ali Bigdeli, Mostafa Ghaderi-Zefrehei, Bluma J Lesch, Mehrdad Behmanesh, S Shahriar Arab

“…To this end, we simultaneously analyzed both protein structures and amino acid sequences from viral and bacterial proteins and compared them to MOG and MBP. …”
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