Construction of a novel radioresistance-related signature for prediction of prognosis, immune microenvironment and anti-tumour drug sensitivity in non-small cell lung cancer by Yanliang Chen, Chan Zhou, Xiaoqiao Zhang, Min Chen, Meifang Wang, Lisha Zhang, Yanhui Chen, Litao Huang, Junjun Sun, Dandan Wang, Yong Chen

“…Subsequently, an eight-gene (APOBEC3B, DOCK4, IER5L, LBH, LY6K, RERG, RMDN2 and TSPAN2) risk score model was established and demonstrated to be an independent prognostic factor in NSCLC on the basis of Cox regression analysis. …”
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Integrated analysis of bioinformatics, mendelian randomization, and experimental validation reveals novel diagnostic and therapeutic targets for osteoarthritis: progesterone as a p... by Ziyu Weng, Chenzhong Wang, Bo Liu, Yi Yang, Yueqi Zhang, Chi Zhang

“…Screening with the Drug Signatures Database (DSigDB) identified progesterone as a small-molecule drug targeting these key proteins. Molecular docking analysis using AutoDock Vina revealed that progesterone exhibited binding energies of ≤ -7 kcal/mol with each of the key proteins, indicating strong binding affinity. …”
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Bis(7)-harmine derivatives as potential multi-target anti-Alzheimer agents by Hongtao Du, Hongtao Du, Hongtao Du, Fang Ma, Fang Ma, Yuanyuan Cao, Miaoyan Bai, Xinyi Gao, Ziyi Yang, Yang Xu, Yan Yan, Yan Yan

“…The cytotoxicity was evaluated using the MTT assay. The Surflex-Dock program in Sybyl-X2.0 Software was employed for molecular docking.ResultsIn vitro studies revealed that numerous synthesized compounds exhibited potent inhibitory activity against hAChE, and hMAO-B (IC50 < 1 μM), as well as Aβ1−42 aggregation (IC50 < 20 μM). …”
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Synthesis, characterization and biological profile of some new dihydropyrimidinone derivaties by Madiha Kanwal, Humaira Nadeem, Sumra Malik, Saima Maqsood

“…These substances were then subjected to molecular docking studies via Auto dock Vina software to determine their affinity for binding to proteins from different bacterial strains including (Staphylococcus epidermidis (S. epidermidis), Staphylococcus aureus (S. aureus), Mycobacterium luteus (M. luteus), Salmonella typhi (S.typhi), Bacillus subtilis (B. subtilis), and Escherichia coli (E. coli) and fungal (Candida glabrata (C. glabrata), Candida albicans (C. albicans), and Saccharomyces cerevisiae (S. cerevisiae) strains. …”
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Herb5GluCon: A novel polyherbal formulation with dual-action inhibiting properties against oxidative stress and glycoside hydrolases – an in silico and in vitro approach by Abbirami Balachandran, Patrick N. Okechukwu, Baskaran Gunasekaran, Jeleń Małgorzata, Beata Morak-Młodawska, Gabriele R.A. Froemming, Sameer Sapra, Charlie A. Lavilla, Jr., Merell P. Billacura, Salini D. Rajendran, Anis Najwa Abdul Rani, Anand Gaurav

“…Methods: The in silico molecular docking of the compounds were performed using AutoDock Vina 1.2.0. …”
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An allelic atlas of immunoglobulin heavy chain variable regions reveals antibody binding epitope preference resilient to SARS-CoV-2 mutation escape by Weiqi Deng, Weiqi Deng, Xuefeng Niu, Ping He, Ping He, Qihong Yan, Qihong Yan, Huan Liang, Yongping Wang, Yongping Wang, Lishan Ning, Lishan Ning, Zihan Lin, Zihan Lin, Yudi Zhang, Xinwei Zhao, Xinwei Zhao, Liqiang Feng, Linbing Qu, Ling Chen, Ling Chen

“…Binding affinity and neutralizing activity were determined using bio-layer interferometry and pseudovirus neutralization assays. Primary docking was performed using ZDOCK (3.0.2) to generate the initial conformation of the antigen-antibody complex, followed by simulations of the complete conformations using Rosetta SnugDock software. …”
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In silico drug repurposing at the cytoplasmic surface of human aquaporin 1. by Aled R Lloyd, Karl Austin-Muttitt, Jonathan G L Mullins

“…Of the 1512 compounds tested, 1002 docking results were obtained, and 198 of these conformations occupied a position within the intrinsic water pore. 30 compounds with promising docking scores were assessed by MD. …”
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Structural Design and Simulation Analysis of a Kind of Multi-function Intelligent Wheelchair by Wang Shukun, Chen Hui, Huang Yude, Liu Wei

“…Through market research and social investigation,the intelligent wheelchair has the walking function,docking function,lifting function and other auxiliary functions,and the corresponding executing agency is designed. …”
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Tetrahydroxy Cyclic Urea-Potent Inhibitor for HIV-1 Protease Wild Type and Mutant Type—A Computational Design by S. Sree Kanth, M. Vijjulatha

“…The biological activity of these inhibitors were predicted by a model equation generated by the regression analysis between biological activity (log 1/Ki) of known inhibitors and there combined docking scores from six of the wild type protein docking. …”
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In Silico Analysis on the Interaction of Haloacid Dehalogenase from Bacillus cereus IndB1 with 2-Chloroalkanoic Acid Substrates by Enny Ratnaningsih, Saepulloh Saepulloh

“…The docking simulation also indicated that the docking energy differences of two enantiomers of 2-chloroalkanoic acids substrates were not significant. …”
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Τhiazolidine-4-One Derivatives with Variable Modes of Inhibitory Action Against DPP4, a Drug Target with Multiple Activities and Established Role in Diabetes Mellitus Type II by Dionysia Amanatidou, Phaedra Eleftheriou, Anthi Petrou, Athina Geronikaki, Theodoros Lialiaris

“…Inhibition modes of uncompetitive, non-competitive, and mixed type were also identified. Docking analysis was in accordance with the in vitro results, with a linear correlation of logIC₅₀ with a Probability of Binding Factor(PF) derived using docking analysis to a specific target box and to the whole enzyme. …”
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Exploring the Infectious Drug Target Glutathione S-Transferase in Plasmodium falciparum with the Inhibitory Potential of Azadirachta indica Phytocompounds by Esam S. Al-Malki

“…Results are confirmed by the possible re-docking poses by the docking method, and the binding score is used for the evaluations. …”
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Senyawa Fucodiphlorethol Dan Phloroglucinol Alga Coklat Sebagai Inhibitor Lipase Secara In Silico by Yohanes Bare, Dewi Ratih Tirto Sari, Marsiana Coo Mogi, Maria Marcelina Dua Nurak

“…Lipase structure (PDB ID 1ETH) was obtained from protein data bank and docked with fucodiphlorethol and phloroglucinol in specific position. …”
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Intraocular Pressure Changes during Femtosecond Laser-Assisted Cataract Surgery: A Comparison between Two Different Patient Interfaces by Chiara De Giacinto, Rossella D’Aloisio, Alessandro Bova, Tommaso Candian, Alberto Armando Perrotta, Daniele Tognetto

“…After the docking procedure, a statistically significant increase in IOP from the baseline was found in both groups (p<0.001). …”
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Recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in food by Pengfei Chen, Chaoqiong Hu, Xuan Tao, Zheng Zhou, Lijun Wang, Xiao Yang, Zhenming Che, Xianggui Chen, Yukun Huang

“…The interaction between this new aptamer and OPPs were analyzed by molecular docking, microscale thermophoresis, circular dichroism and fluorometric analysis. …”
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Pyoverdine, the Major Siderophore in Pseudomonas aeruginosa, Evades NGAL Recognition by Mary E. Peek, Abhinav Bhatnagar, Nael A. McCarty, Susu M. Zughaier

“…We then employed a molecular modeling approach to simulate the binding of pyoverdine to human NGAL using NGAL’s published crystal structures. The docking of pyoverdine to NGAL predicted nine different docking positions; however, neither apo- nor ferric forms of pyoverdine docked into the ligand-binding site in the calyx of NGAL where siderophores are known to bind. …”
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QSAR modeling of benzoquinone derivatives as 5-lipoxygenase inhibitors by T.K. Shameera Ahamed, Vijisha K. Rajan, K. Muraleedharan

“…Keywords: 5-lipoxygenase, Benzoquinone, 2D-QSAR, 3D-QSAR, Molecular docking…”
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Enhancing Crossdocking for a Green Supply Chain Based on IoT and AI by Raziq Ayoub, El Khaili Mohamed, Zamma Abdellah

“…This study explores the convergence of cross-docking methodologies with advanced technologies such as IoT and AI to enhance the sustainability of supply chains. …”
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Synthesis, Antibacterial, Antioxidant, and Molecular Modeling Studies of Novel [2,3′-Biquinoline]-4-Carboxylic Acid and Quinoline-3-Carbaldehyde Analogs by Zeleke Digafie, Yadessa Melaku, Zerihun Belay, Rajalakshmanan Eswaramoorthy

“…Thus, compounds 4, 9, and 10 showed the best antibacterial activities in both in vitro and molecular docking analyses among the synthetic compounds. The results of in silico molecular docking evaluation of the synthetic compounds against E. coli DNA gyrase B were in good agreement with the in vitro antibacterial analysis. …”
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Active ingredients and mechanisms of peony seed blended oil in diabetes treatment using Kunming mice: Insights from GC–MS, network pharmacology, and experimental verification by Yuning Gu, Fengliang Zhong, Tiantian Sun, Zirui Chang

“…This study aimed to evaluate the combined hypoglycemic potential of these oils through in vitro and in vivo experiments, supported by network pharmacology and molecular docking analyses to explore the underlying mechanisms. …”
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