Machine learning-powered, high-affinity modification strategies for aptamers by Gubu Amu, Xin Yang, Hang Luo, Sifan Yu, Huarui Zhang, Yuan Tian, Yuanyuan Yu, Shijian Ding, Yufei Pan, Zefeng Chen, Yixin He, Yuan Ma, Baoting Zhang, Ge Zhang, YANG XIN

“…This approach harnessed the power of machine learning to predict the most promising high-affinity modification strategy for aptamers.…”
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Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways. by Andreas R Pfenning, Tae-Kyung Kim, James M Spotts, Martin Hemberg, Dan Su, Anne E West

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Thlaspi arvense suppresses gut microbiota related TNF inflammatory pathway to alleviates ulcerative colitis by Wenkai Wang, Yiyang Zhao, Ziwei Wang, Chaowei Wang, Ling Bi, Yan Wang, Yan Wang

“…Consistent with experimental data, PPI and KEGG analyses implicated TNF-α, IL-6, and AKT as key targets, primarily through TNF signaling pathway modulation. To validate these predictions, molecular docking confirmed stable interactions between TA compounds and identified targets, while dynamics simulations specifically emphasized isovitexin’s high affinity for TNF-α. …”
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Pericarpium Trichosanthis Injection Protects Isoproterenol-Induced Acute Myocardial Ischemia via Suppressing Inflammatory Damage and Apoptosis Pathways by Zizheng Wu, Xing Chen, Jiahao Ye, Xiaoyi Wang, Zhixi Hu

“…The multimodal methodology is designed to comprehensively uncover the therapeutic benefits and molecular pathways underlying this traditional Chinese medicine formulation. …”
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Identification of novel drug targets for Helicobacter pylori: structure-based virtual screening of potential inhibitors against DAH7PS protein involved in the shikimate pathway by Narjes Noori Goodarzi, Narjes Noori Goodarzi, Mahshid Khazani Asforooshani, Mahshid Khazani Asforooshani, Behzad Shahbazi, Nayereh Rezaie Rahimi, Nayereh Rezaie Rahimi, Farzad Badmasti

“…The DAH7PS protein involved in the shikimate pathway was selected for the structure-based virtual screening (SBVS) approach. …”
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Neuroendocrine tumors of the digestive system: pathologic and molecular characteristics by V. V. Delektorskaya

“…Additionally, data on key signaling pathways and potential predictive molecular markers involved in the development of neuroendocrine tumors of the gastrointestinal tract and pancreas are presented in this review. …”
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Exploration potential sepsis–ferroptosis mechanisms through the use of CETSA technology and network pharmacology by Yu Zhou Shen, Bin Luo, Qian Zhang, Li Hu, Ying Chun Hu, Mu Hu Chen

“…Go analysis showed that monomeric small molecule Licochalcone D could regulate the process of intracellular enzyme system. The KEGG pathway analysis showed that the signal pathway of the main effect was related to the calcium pathway. …”
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Network toxicology combined with molecular docking technology to explore the molecular mechanism of amatoxin causing liver injury by Chenglin Wang, Xin Wang, Yaxing Deng, Yingchun Hu, Li Hu

“…PPI network topology revealed critical nodal connections, while functional enrichment analyses delineated key biological processes and signaling pathways associated with these targets. Molecular docking simulations demonstrated high-affinity binding between amatoxin and both SP1 and CNR1, suggesting direct mechanistic interactions. …”
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Analyzing mechanisms of qing fei bao yuan decoction granules in treating COPD based on LC-MS, network pharmacology and in vivo methods by Amei Tang, Yang Liu, Guoqiang Guan, Tong Hao, Feng Cao

“…Disease- and drug-specific targets were collated from a plethora of databases, including Batman-TCM, Stitch, Swiss Target Prediction and GeneCards. GO and KEGG pathways were analyzed for the collected targets. …”
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Computational Evaluation and Multi-Criteria Optimization of Natural Compound Analogs Targeting SARS-CoV-2 Proteases by Paul Andrei Negru, Andrei-Flavius Radu, Ada Radu, Delia Mirela Tit, Gabriela Bungau

“…CHEMBL1495225 establishes multiple hydrogen bonds with the 3CLpro residues ASP197, ARG131, TYR239, LEU272, and GLY195, along with hydrophobic contacts with LEU287. Gene expression predictions via DIGEP-Pred indicated that the top-ranked compounds could influence biological pathways linked to inflammation and oxidative stress, processes implicated in COVID-19’s pathology. …”
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Identification of Exosome-Associated Biomarkers in Diabetic Foot Ulcers: A Bioinformatics Analysis and Experimental Validation by Tianbo Li, Lei Gao, Jiangning Wang

“…Transcription factor and miRNA predictions uncovered regulatory circuits, and DGIdb-driven drug repurposing followed by molecular docking identified Indatuximab ravtansine and heparin as high-affinity SDC1 binders. …”
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Molecular Mechanism of the Effect of Huanglian Jiedu Decoction on Type 2 Diabetes Mellitus Based on Network Pharmacology and Molecular Docking by Bei Yin, Yi-Ming Bi, Guan-Jie Fan, Ya-Qing Xia

“…These results were validated by molecular docking, which identified 5 high-affinity active components in HLJDD, including quercetin, wogonin, baicalein, kaempferol, and oroxylin A. …”
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Neutrophil extracellular traps drive osteoporosis via NCF2-dependent signaling: integrated transcriptomics with mechanistic validation by Xiangyun Guo, Liang Wang, Shuangliu Chen, Chuanrui Sun, Jinran Qin, Qingqing Liu, Yiwen Gan, Yan Li, Zikai Jin, Xu Wei, Yili Zhang

“…Knockdown of NCF2 reduced NETs formation in neutrophil-like cells and alleviated NETs-induced osteoblast differentiation impairment. Drug prediction and molecular docking analyses demonstrated high affinity and pharmacological potential targeting these genes.Conclusions This study unveils the link between NETs formation and OP, highlighting NCF2 as crucial players. …”
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Respiratory toxicity mechanism of 6PPD and 6PPD-quinone: An integrated study based on network toxicology and molecular docking by Gang Li, Dan Li, Weibin Zhai, Chang Liu, Mengying Chen, Qingqiang Xu, Yuanlan Huang

“…Respiratory hazard potential was predicted using ADMETlab 3.0 and ProTox-II. Potential targets were identified through multi-database mining (BindingDB, ChEMBL, SwissTargetPrediction, TargetNet), with disease-associated targets categorized into acute and chronic respiratory damage using GeneCards and OMIM. …”
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Cornus officinalis Protects Against Steroid-Induced Osteonecrosis of the Femoral Head Through Inhibiting Inflammatory Responses and Apoptosis via Network Pharmacology and Experimen... by Wang Y, Fan Y, Li M, Song Z, Wang P, Xie F, Miao Y, Wang Y, Zhang P, Zhan Q

“…The protein–protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses were performed to predict the core targets and pathways of SZY in the treatment of SONFH. …”
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Integrating network pharmacology and molecular modeling to decipher the anti-esophageal squamous cell carcinoma mechanisms of Bidens pilosa L by Zhenzhen Yang, Cheng Chang, Na Gao, Pan Gao, Yinsen Song, Ruiting Feng, Jingjie Meng, Chen Wang, Haozhe Zhang, Tianli Fan

“…Functional enrichment analysis highlighted significant involvement in cellular responses to hormone stimuli, nitrogen compounds, and phosphorylation, with key pathways including cancer, PI3K-Akt, and Ras signaling. …”
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