Benchmarking protein language models for protein crystallization by Raghvendra Mall, Rahul Kaushik, Zachary A. Martinez, Matt W. Thomson, Filippo Castiglione

“…Abstract The problem of protein structure determination is usually solved by X-ray crystallography. …”
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CryoEM structure and small-angle X-ray scattering analyses of porcine retinol-binding protein 3 by Vineeta Kaushik, Luca Gessa, Nelam Kumar, Matyáš Pinkas, Mariusz Czarnocki-Cieciura, Krzysztof Palczewski, Jiří Nováček, Humberto Fernandes

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Evolutionary Insights into IL17A in Lagomorphs by Fabiana Neves, Joana Abrantes, Tereza Almeida, Paulo P. Costa, Pedro J. Esteves

“…The differences observed between leporids and humans or rodents might also represent important alterations in protein structure and function. In addition, as for other interleukins, IL17A sequences of human and European rabbit are more closely related than the sequences of human and mouse or European rabbit and mouse. …”
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The amino acids differences in epitopes may promote the different allergenicity of ovomucoid derived from hen eggs and quail eggs by Mengzhen Hao, Shuai Yang, Shiwen Han, Huilian Che

“…The difference in sensitization compare to hen egg ovomucoid may be due to amino acids differences affecting protein structure by changing antigenic epitopes.…”
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Effects of Naringenin and Its Glycosides on Functional Properties of Oat Protein and Their Interaction Mechanism by Wuzhen LIU, Ti LI, Qin GENG, Jun CHEN, Jialong HAN, Chengmei LIU, Taotao DAI

“…To investigate the effect of naringenin and its glycoside (naringin and narirutin) on foaming, emulsifying and interfacial tension of oat protein and their interaction mechanism, in this study, fluorescence spectra and circular dichroism were used to elucidate the interaction mechanism and protein structure changes of oat protein-flavonoid complex system. …”
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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 Expression of <i>unc-13d</i> in the Sex Reversal of <i>Monopterus albus</i> by Zitong Lian, Fang Meng, Xueping Xia, Junchao Fang, Haifeng Tian, Qiaomu Hu

“…In this study, we firstly cloned and characterized the sequence and protein structure of <i>unc-13d</i> of <i>M. albus.</i> We found that the genomic structure of <i>unc-13d</i> was different from other species. …”
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In Silico Analysis Revealed Five Novel High-Risk Single-Nucleotide Polymorphisms (rs200384291, rs201163886, rs193141883, rs201139487, and rs201723157) in ELANE Gene Causing Autosom... by Khyber Shinwari, Mikhail A. Bolkov, Muhammad Yasir Akbar, Liu Guojun, Svetlana S. Deryabina, Irina A. Tuzankina, Valery. A. Chereshnev

“…We identified the deleterious nsSNPs, constructed mutant protein structures, and evaluated the impact of mutation by employing molecular docking. …”
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Effect of Composition and Processing Conditions on Selected Properties of Potato-Based Pellets and Microwave-Expanded Snacks Supplemented with Fresh Beetroot Pulp by Katarzyna Lisiecka, Agnieszka Wójtowicz, Agnieszka Sujak

“…This indicates that the protein structure underwent some form of ordering as the molecular interactions of the proteins intensified. …”
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Predicting deamidation and isomerization sites in therapeutic antibodies using structure-based in silico approaches by David Hoffmann, Joschka Bauer, Markus Kossner, Andrew Henry, Anne R. Karow-Zwick, Giuseppe Licari

“…The predictive accuracy of the model was evaluated for four different states of the protein structure: (1) static homology models, (2) enhancing low-frequency vibrational modes during short molecular dynamics (MD) runs, (3) a combination of (2) with a protonation state reassignment, and (4) conventional full-atomistic MD simulations. …”
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Unveiling the new chapter in nanobody engineering: advances in traditional construction and AI-driven optimization by Jiwei Liu, Lei Wu, Anqi Xie, Weici Liu, Zhao He, Yuan Wan, Wenjun Mao

“…AI’s exceptional performance in protein structure prediction and molecular interaction simulation has introduced novel perspectives and tools for Nb design and optimization. …”
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A survey of the Sli gene in wild and cultivated potato by Mercedes Ames, Andy Hamernik, William Behling, David S. Douches, Dennis A. Halterman, Paul C. Bethke

“…In silico analysis of Sli protein structure did not support the hypothesis that amino acid changes from wild‐type (no insertion) to insertion‐type account for changes in protein function. …”
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AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins by Olivia S. Pratt, Luc G. Elliott, Margaux Haon, Shahram Mesdaghi, Rebecca M. Price, Adam J. Simpkin, Daniel J. Rigden

“…AlphaFold 2 (AF2) has revolutionised protein structure prediction but, like any new tool, its performance on specific classes of targets, especially those potentially under-represented in its training data, merits attention. …”
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Molecular Detection and Genetic Characterization of Avian Leukosis Virus From Field Outbreaks in Bangladesh by Md. Golzar Hossain, Riman Pathan, SM Nazmul Hasan, Anandha Mozumder, Moslema Jahan Mou, Marjana Akter, Chandan Sikder, Riyan Al Islam Reshad, Roni Mia, Sukumar Saha, Tofazzal Islam, Sharmin Akter

“…Mutational analysis indicated several mutations throughout the envelope glycoprotein of the identified strains. Protein structure analysis showed minor changes in the hydrophobic region of the envelope protein of the identified strains. …”
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Prospective de novo drug design with deep interactome learning by Kenneth Atz, Leandro Cotos, Clemens Isert, Maria Håkansson, Dorota Focht, Mattis Hilleke, David F. Nippa, Michael Iff, Jann Ledergerber, Carl C. G. Schiebroek, Valentina Romeo, Jan A. Hiss, Daniel Merk, Petra Schneider, Bernd Kuhn, Uwe Grether, Gisbert Schneider

“…In order to proactively evaluate the deep interactome learning framework for protein structure-based drug design, potential new ligands targeting the binding site of the human peroxisome proliferator-activated receptor (PPAR) subtype gamma are generated. …”
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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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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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