Development of a multi-epitope chimeric vaccine in silico against Babesia bovis, Theileria annulata, and Anaplasma marginale using computational biology tools and reverse vaccinolo... by Amam Zonaed Siddiki, Sabreena Alam, Farhan Fuad Bin Hossen, Md Abdul Alim

“…Following that, we performed molecular docking of the refined chimeric vaccine construct with Rp-105 and TLR-9. …”
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Synthesis and Evaluation of the Acetylcholinesterase Inhibitory Activities of Some Flavonoids Derived from Naringenin by The-Huan Tran, Thi-Thu-Hien Vo, Thi-Quynh-Nhi Vo, Thi-Cam-Nhung Cao, Thai-Son Tran

“…The evaluation of AChE inhibitory activity by the Ellman method showed that there were four substances (2, 4, 5, and 7) with relatively good biological activities (IC50 < 100 μM), and these biological activities were better than that of naringenin. The molecular docking revealed that strong interactions with amino acid residue Ser200 of the catalytic triad and those of the peripheral region of the enzyme were crucial for strong effects against AChE. …”
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High-Throughput Screening and Molecular Dynamics Simulation of Natural Products for the Identification of Anticancer Agents against MCM7 Protein by Xin Zhang, Hui Chen, Hui Lin, Ronglan Wen, Fan Yang

“…For this objective, a molecular docking and molecular dynamics (MD) simulation-based virtual screening of 29,000 NPASS library was carried out. …”
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Virtual screening and molecular dynamics simulations identify repurposed drugs as potent inhibitors of Histone deacetylase 1: Implication in cancer therapeutics. by Mohammed Alrouji, Sabina Yasmin, Mohammed S Alshammari, Fahad A Alhumaydhi, Sharaf E Sharaf, Moyad Shahwan, Anas Shamsi

“…We conducted a series of analyses, including molecular docking, drug profiling, PASS evaluation, and interaction analysis. …”
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Integrated in silico and in vitro exploration of the anti-VEGFR-2 activities of a semisynthetic xanthine alkaloid inhibiting breast cancer. by Eslam B Elkaeed, Hazem Elkady, Ahmed M Khattab, Reda G Yousef, Hanan A Al-Ghulikah, Dalal Z Husein, Ibrahim M Ibrahim, Mohamed A Elkady, Ahmed M Metwaly, Ibrahim H Eissa

“…T-1-NBAB's potential to interacts with and inhibit the VEGFR-2 was indicated using in silico techniques like molecular docking, MD simulations, MM-GBSA, PLIP, essential dynamics, and bi-dimensional projection experiments. …”
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Insilico targeting of virus entry facilitator NRP1 to block SARS-CoV2 entry. by Nousheen Bibi, Maleeha Shah, Shahzad Khan, Muhammad Shahzad Chohan, Mohammad Amjad Kamal

“…Following virtual screening, docking studies, and evaluation of binding affinity and ADMET properties, 10 compounds were shortlisted. …”
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Identification of Diagnostic Genes and Effective Drugs Associated with Osteoporosis Treatment by Single-Cell RNA-Seq Analysis and Network Pharmacology by Zhanyue Zhang, Tingbao Zhang, Liangshuang Zhou, Jianzhong Guan

“…Key drugs were determined by proteins-proteins interaction and molecular docking. Results. Firstly, 15,577 cells were obtained, and 12 cell subpopulations were identified by clustering, among which 6 cell subpopulations belong to CD45+ BM-MSCs and the other subpopulations were CD45-BM-MSCs. …”
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Cuproptosis genes in predicting the occurrence of allergic rhinitis and pharmacological treatment. by Ting Yi

“…Finally, AR signature genes were used as targets for drug prediction and molecular docking to identify candidate drugs that may affect SAR.…”
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Modulatory effects of cinnamomi cortex and its components epicatechin and linalool on skin circadian rhythms by Ji-Young Kim, Juyeon Lee, Soo-Hyeon Lee, Eui-Man Jung, Kyung-Ha Lee

“…Gene expression analysis revealed that CC extract, EC, and LO altered the mRNA and protein levels of clock genes in a time-dependent manner. During molecular docking simulations, both EC and LO exhibited strong binding affinities for RORA, a key nuclear receptor involved in circadian regulation. …”
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Immunoinformatic approach to the design of a novel multi-epitope vaccine against Leishmania major fused to human IgG-Fc by Mahmood Fadaie, Zabihollah Shahmoradi, Hossein Khanahmad

“…To investigate how the MEV-Fc vaccine interacts with Toll-like receptors, molecular docking, multi-scale normal mode analysis simulation, and computational immune simulation were employed to study humoral and cellular immune responses. …”
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Narrowing the gap between machine learning scoring functions and free energy perturbation using augmented data by Ísak Valsson, Matthew T. Warren, Charlotte M. Deane, Aniket Magarkar, Garrett M. Morris, Philip C. Biggin

“…Moreover, we demonstrate how leveraging augmented data (generated using template-based modelling or molecular docking) can significantly improve binding affinity prediction correlation and ranking on the FEP benchmark (weighted mean PCC and Kendall’s τ increases from 0.41 and 0.26 to 0.59 and 0.42). …”
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In silico study about β-amyloid’s role in Alzheimer’s disease and glaucoma and prediction of its interactions with glaucoma related proteins by Nancy Maurya

“…The computational tool called Hex 8.0.0 has been used in this work. Results: The docking score for β-amyloid and myocilin was found to be –724.1 kJ mol–1 while that for β-amyloid and wild-type optineurin pair was found to be –296.9 kJ mol–1 and that for β-amyloid and mutated optineurin was –607.1 kJ mol–1. …”
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Rab7 Investigation Insights into the Existence of White Spot Syndrome Virus in Crustaceans: An In Silico Approach by Mehedi Mahmudul Hasan, M. Nazmul Hoque, Md Robiul Hasan, Mohammad Asaduzzaman, Farha Matin Juliana

“…Homology modeling of Rab7 proteins from different organisms was done using SWISS-MODEL and validated further by developing Ramachandran plots. Protein-protein docking showed that active residues were there in the binding interfaces of Rab7 from organisms of seven different phyla and VP28 of WSSV. …”
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Vision-Based Object Recognition and Precise Localization for Space Body Control by Zeyu Shangguan, Lingyu Wang, Jianquan Zhang, Wenbo Dong

“…The space motion control is an important issue on space robot, rendezvous and docking, small satellite formation, and some on-orbit services. …”
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Elucidating the potential of EGFR mutated NSCLC and identifying its multitargeted inhibitors by Anakha D. Rajeeve, Ramasamy Yamuna, P. K. Krishnan Namboori

“…Since curcumin and CB[2]UN support various medicinal applications in drug delivery and design, we investigated the effect of curcumin and CB[2]UN-based drugs in controlling EGFR-mutant NSCLC through a dodecagonal computational approach. Molecular docking studies revealed that the ligands curcumin (-6.9 kcal/mol) and CB[2]UN (-8.1 kcal/mol) bound more strongly to the EGFR-mutant NSCLC proteins with 2ITX and 2ITV, respectively. …”
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Comprehensive Assessment of Biomolecular Interactions of Morpholine-Based Mixed Ligand Cu(II) and Zn(II) Complexes of 2,2′-Bipyridine as Potential Anticancer and SARS-CoV-2 Agents:... by Karunganathan Sakthikumar, Rui Werner Maçedo Krause, Bienfait Kabuyaya Isamura

“…Density FunctionalTheory (DFT) and molecular docking calculations were relied on to unveil the electronic structure, reactivity, and interacting capability of all substances with DNA, BSA, and SARS-CoV-2 main protease (Mpro). …”
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Computer Simulation on Analgesic Functional Chemome Characteristics of <italic>Radix Saposhnikoviae</italic> by Chunsong ZHENG, Xiaojie XU, Hongzhi YE, Jinxia YE, Guangwen WU, Xianxiang LIU

“…The analgesic functional chemome of RS was identified by molecular docking. The drug/drug-like molecules correlated to p38, TNF-α, iNOS and PDE-4A were retrieved from therapeutic targets database (TTD). …”
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Synthesis, In Silico, and Biological Applications of Novel Heteroleptic Copper (II) Complex of Natural Product-Based Semicarbazone Ligands by Fekadu Muleta, Tegene Desalegn

“…The [Cu(L1) (L2)] complex also shows better antiradical potential (63.7%). Furthermore, the docking result of prepared compounds on S. aureus gyrase confirms the ligands (L1 and L2) and the complex potential molecules possess the smallest binding potential of −8.0 to −8.4 kcal/mol. …”
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Anti-proliferative and photodynamic activities of Senna didymobotrya (Fresen.) leaf alkaloid-rich extracts against breast cancer cells by Kolawole A. Olofinsan, Heidi Abrahamse, Blassan P. George

“…Moreover, the molecular docking analysis revealed the involvement of only hydrophobic bonds in the interactions of the plant’s alkaloid-derived phytoconstituents’ with selected cancer protein biomarkers. …”
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Wedelolactone Mitigates Alcoholic Steatohepatitis via Modulating the TLR4/MyD88/NF-κB Pathway by Tao Jiang, Bingde Hu, Yongxia Li, Shuihong Yu

“…Network pharmacology analysis identified the toll-like receptor 4 (TLR4) pathway as the primary target of WEL in treating ASH. Molecular docking simulations demonstrated WEL’s strong binding affinity with TLR4. …”
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