Computational electrostatic engineering of nanobodies for enhanced SARS−CoV−2 receptor binding domain recognition by Zafar Iqbal, Muhammad Asim, Umair Ahmad Khan, Neelam Sultan, Irfan Ali

“…Surface analyses confirmed optimized electrostatic patches and reduced aggregation propensity in the engineered Nb. This integrated EC and structural engineering approach successfully developed engineered Nbs with enhanced binding specificity, increased thermostability, and reduced aggregation, laying the groundwork for novel therapeutic applications targeting the SARS-CoV-2 spike protein.…”
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HPD is an RNA‐Binding Protein Sustaining Ovarian Cancer Cell Glycolysis, Tumor Growth, and Drug Resistance by Fei Xie, Han Zhang, Xintong Dai, Mengxin Tu, Chenxi Yu, Lumeng Liu, Yajuan Guo, Huanran Sun, Qingle Gao, Jiyan Wang, Mingming Sun, Qijun Zhang, Taoyuan Wang, Tao He, Zhen Li, Yanping Li, Tao Wang, Jianguo Zhao, Zhongjie Chen, Chunze Zhang, Shuai Zhang, Changliang Shan

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Lopinavir and Ritonavir have High Affinity Toward the SARS-CoV-2 S-protein Receptor-binding Domain Sequenced in Brazil by Aline Diogo Marinho, Helyson Lucas Bezerra Braz, João Alison de Moraes Silveira, Danilo Galvão Rocha, Roberta Jeane Bezerra Jorge, Geanne Matos de Andrade

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CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments by Ashley J. Waardenberg, Bassett Maya, Romaric Bouveret, Richard P. Harvey

“…However, determining differential GO and pathway enrichment between DNA-binding experiments or using the GO structure to classify experiments has received little attention. …”
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Chlorophyll a/b-binding Overexpression 2 regulates nitric oxide signaling in Arabidopsis response to sulfur deficiency by Oluwaseun Olayemi Aluko, Zhixin Liu, Yaping Zhou, Hao Liu, Aizhi Qin, Qianli Zhao, Mengfan Li, Chunyang Li, Luyao Kong, Lulu Yan, Vincent Ninkuu, Jean-David Rochaix, Lam-Son Phan Tran, Xuwu Sun

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Association Between Retinol-Binding Protein 4 Levels and Hepatitis C Virus Infection: A Meta-Analysis by Yingying Lin, Xinyu Cui, Na Zhu, Yanyan Li, Peng Wang, Xin Wang, Yunyun Yi, Xin Li

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Dact1 induces Dishevelled oligomerization to facilitate binding partner switch and signalosome formation during convergent extension by Allyson Angermeier, Deli Yu, Yali Huang, Sylvie Marchetto, Jean-Paul Borg, Chenbei Chang, Jianbo Wang

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A protective and broadly binding antibody class engages the influenza virus hemagglutinin head at its stem interface by Holly C. Simmons, Joel Finney, Ryutaro Kotaki, Yu Adachi, Annie Park Moseman, Akiko Watanabe, Shengli Song, Lindsey R. Robinson-McCarthy, Valerie Le Sage, Masayuki Kuraoka, E. Ashley Moseman, Garnett Kelsoe, Yoshimasa Takahashi, Kevin R. McCarthy

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Computational insights into the inhibitory effects of PFAS 14 on colorectal cancer targeting GSTA1 through competitive binding by Jinxiao Li, Yanran Wu, Pian Ye, Dongmei Zuo, Shuangjiao Deng, Ran Pang, Huarong Li

“…Computational analysis revealed that PFAS 14 exhibits high binding affinity for GSTA1, occupying its glutathione-binding site. …”
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Exploring the characters of sperm lipid peroxidation, enzymatic antioxidant activity, and spermatozoa zona binding capacity with aging in dogs by Kenneth Owoicho Abah, Zuzanna Ligocka-Kowalczyk, Agnieszka Partyka, Sylwia Prochowska, Alain Fontbonne, Wojciech Niżański

“…Mature dogs exhibited significantly higher total motility, sperm concentration, TSC, membrane integrity, and zona binding capacity compared to senile dogs (P < 0.05). …”
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Exploring the roles and molecular mechanisms of RNA binding proteins in the sorting of noncoding RNAs into exosomes during tumor progression by Ting Wang, Hui Zhang

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Pleiotropic expression quantitative trait loci are enriched in enhancers and transcription factor binding sites and impact more genes by Aitor González, Pascale Paul

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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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NanoBinder: a machine learning assisted nanobody binding prediction tool using Rosetta energy scores by Palistha Shrestha, Chandana S. Talwar, Jeevan Kandel, Kwang-Hyun Park, Kil To Chong, Eui-Jeon Woo, Hilal Tayara

“…To address current challenges in nanobody design, we introduce NanoBinder, an interpretable machine learning model that predicts nanobody-antigen binding using Rosetta energy scores. NanoBinder utilizes a Random Forest model trained on experimentally validated complexes and can be seamlessly integrated into the Rosetta software. …”
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A broad-spectrum antibiotic targets multiple-drug-resistant bacteria with dual binding targets and no detectable resistance by Wenyan He, Xueting Huan, Yinchuan Li, Qisen Deng, Tao Chen, Wen Xiao, Yijun Chen, Lingman Ma, Nan Liu, Zhuo Shang, Zongqiang Wang

“…Abstract The rapid emergence of difficult-to-treat multidrug-resistant pathogens, combined with the scarcity of antibiotics possessing novel mechanisms, poses a significant threat to global public health. Here, we integrate the synthetic-bioinformatic natural product approach with peptide optimization to unveil the antibiotic-producing potential of Paenibacillaceae bacteria. …”
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Structural basis for C. elegans pairing center DNA binding specificity by the ZIM/HIM-8 family proteins by Meili Li, Chengming Zhu, Zheng Xu, Mingjing Xu, Yan Kuang, Xinhao Hou, Xinya Huang, Mengqi Lv, Yongrui Liu, Yong Zhang, Ziyan Xu, Xu Han, Suman Wang, Yunyu Shi, Shouhong Guang, Fudong Li

“…These structures demonstrated the ZF1-2-CTD folds as an integrated structural unit crucial for its DNA binding specificity. …”
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Mechanistic insights into Alpha-Synuclein binding to P2RX7: A molecular dynamic and docking study. by Mukesh Kumar, Kanchan Singh, Jayant Joshi, Shreya Sharma, Amit Kumar, Karuna Irungbam, Manish Mahawar, Mohini Saini

“…Activation of P2RX7 by αSyn is implicated in neuronal degeneration, potentially causing pore dilation and increased inflammation. By integrating the data curation, molecular docking, and molecular dynamics (MD) simulations, along with structural analyses, we attempted to elucidate the molecular mechanisms and binding sites for P2RX7-αSyn interaction. …”
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In-feed provision of binding proteins sustains piglet gut health and mitigates ETEC-induced post-weaning diarrhea by Jiajia Xu, Melania Andrani, Rikke Brødsgaard Kjærup, Tina Sørensen Dalgaard, Carsten Eriksen, Andreas Hougaard Laustsen, Susanne Brix, Sandra Wingaard Thrane, Nuria Canibe

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Not all conservation “policy” is created equally: When does a policy give rise to legally binding obligations? by Justine Bell‐James, Rose Foster, Miguel Frohlich, Carla Archibald, Claudia Benham, Megan Evans, Pedro Fidelman, Tiffany Morrison, Liza Rolim Baggio, Peter Billings, Nicole Shumway

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Characterization of binding affinity changes of SARS-CoV-2 omicron variant peptides to population-specific HLA by Che-Mai Chang, Chang-Jiun Wu, Maxim Shkurnikov, Chin-Lin Guo, Wan-Chen Huang, Alexander Tonevitsky, Wei-Chiao Chang

“…Results Our findings revealed that mutations in the Spike protein had a more pronounced effect on HLA class II binding affinities than on HLA class I. While binding affinity profiles for HLA class I were largely consistent across populations, significant population-specific variations were observed for HLA class II alleles. …”
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