In Silico Study of Coumarins: Wedelolactone as a Potential Inhibitor of the Spike Protein of the SARS-CoV-2 Variants by Saurav Katuwal, Siddha Raj Upadhyaya, Rishab Marahatha, Asmita Shrestha, Bishnu P. Regmi, Karan Khadayat, Saroj Basnet, Ram Chandra Basnyat, Niranjan Parajuli

“…Furthermore, coarse-grained molecular dynamics (MD) simulation studies of spike protein-wedelolactone complexes validated the stable binding of wedelolactone in the respective binding pockets. …”
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Superhydrophobic property of cement mortar with polydimethylsiloxane modifier and a rough surface by Siyu Yu, Li Li, Chao Zhou, Song Lan

“…Hydrophobic modified HUHPC has sufficient mechanical properties to meet engineering requirements. Molecular dynamics simulations validates the mechanism of superhydrophobicity. …”
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Binding Orientations and Lipid Interactions of Human Amylin at Zwitterionic and Anionic Lipid Bilayers by Zhenyu Qian, Yan Jia, Guanghong Wei

“…In this study, as a first step to understand the mechanism of membrane-mediated hIAPP aggregation, we investigate the binding behaviors of hIAPP monomer at zwitterionic palmitoyloleoyl-phosphatidylcholine (POPC) bilayer by performing atomistic molecular dynamics simulations. The results are compared with those of hIAPP at anionic palmitoyloleoyl-phosphatidylglycerol (POPG) bilayers. …”
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Interaction of toll-like receptors and ACE-2 with different variants of SARS-CoV-2: A computational analysis by Azadeh Zahmatkesh, Elham Salmasi, Reza Gholizadeh

“…Molecular docking and molecular dynamics (MD) simulations were performed to investigate receptor-ligand interactions. …”
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Effect of SiO2 on thermal conductivity of methane by Yuanchao LIU, Tingting ZHAO, Xinhao LIU, Yuanning WANG

“…In view of the lack of research on the microscopic thermal conductivity mechanism in the formation of methane hydrate in porous media, a molecular dynamics method was proposed to simulate the porous media gap model composed of SiO2. …”
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Study on Molecular Recognition between Euphorbia Factor L713283 and β-Tubulin via Molecular Simulation Methods by Shan Chang, Hong-qiu He, Ren Kong, Zhen-jian Xie, Jian-ping Hu

“…We further investigated the binding modes of L713283 with β-tubulin using molecular docking and molecular dynamics (MD) simulation methods. The results indicated that the binding site between β-tubulin and L713283 was composed of the four regions, that is, residues Phe20~Glu27, Leu225~Thr232, Phe270~Gly277, and Ile356~Met363. …”
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On the validity of some equilibrium models for thermodiffusion by Araujo-Rocha, Mario, Diaz-Marquez, Alejandro, Stirnemann, Guillaume

“…Notably, there have been some attempts to relate this non-equilibrium, steady-state manifestation, to equilibrium properties of these solutions, for example, to the temperature dependence of the self-diffusion coefficient or to the solvation free energies of each of their components. Here, we use molecular dynamics simulations on dilute solutions containing molecular-size solutes, both in a thermophoretic setting as well as under equilibrium conditions, to test the validity of such models. …”
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Exploring transition states of protein conformational changes via out-of-distribution detection in the hyperspherical latent space by Bojun Liu, Jordan G. Boysen, Ilona Christy Unarta, Xuefeng Du, Yixuan Li, Xuhui Huang

“…Markov state models (MSMs), built from Molecular Dynamics (MD) simulations, capture these dynamics through transitions among metastable conformational states, and have demonstrated success in studying protein conformational changes. …”
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Detailed Photoisomerization Dynamics of a Green Fluorescent Protein Chromophore Based Molecular Switch by Chen-Wei Jiang, Ai-Ping Fang, Di Zhao, Hong-Rong Li, Rui-Hua Xie, Fu-Li Li

“…With density-functional-based nonadiabatic molecular dynamics simulations, trans-to-cis and cis-to-trans photoisomerizations of a green fluorescent protein chromophore based molecule 4-benzylidene-2-methyloxazol-5(4H)-one (BMH) induced by the excitation to its S1 excited state were performed. …”
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High-throughput single-molecule quantification of individual base stacking energies in nucleic acids by Jibin Abraham Punnoose, Kevin J. Thomas, Arun Richard Chandrasekaran, Javier Vilcapoma, Andrew Hayden, Kacey Kilpatrick, Sweta Vangaveti, Alan Chen, Thomas Banco, Ken Halvorsen

“…We experimentally show that base stacking can influence stability of a DNA nanostructure, modulate kinetics of enzymatic ligation, and assess accuracy of force fields in molecular dynamics simulations. Our results provide insights into fundamental DNA interactions that are critical in biology and can inform design in biotechnology applications.…”
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Drug inhibition and substrate transport mechanisms of human VMAT2 by Feiwen Wei, Huihui Liu, Wei Zhang, Jufang Wang, Yanqing Zhang

“…Utilizing cryo-electron microscopy (cryo-EM), mutagenesis functional assays, and molecular dynamics (MD) simulations, we elucidate the mechanisms of substrate transport and drug inhibition. …”
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Exploring pyrazolines as potential inhibitors of NSP3-macrodomain of SARS-CoV-2: synthesis and in silico analysis by Rekha Joshi, Harsh Gaikwad, Bhavana Soge, Abdulrahman Alshammari, Norah A. Albekairi, Atul Kabra, Usha Yashwante, Baban Kolte, Pradip Lokhande, Rohan J Meshram

“…We identified the NSP3-microdomain (Mac-1) of SARS-CoV-2 as a putative target for newly synthesized triaryl-2-pyrazoline compounds. The molecular dynamics simulation-based free energy estimation suggests compounds 7a, 7d, 7 g, 7i, 7k, and 7 L as promising Mac-1 inhibitors. …”
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Design of a Multiepitope Pan-Proteomic mRNA Vaccine Construct Against African Swine Fever Virus: A Reverse Vaccinology Approach by Ella Mae Joy S. Sira, Lauren Emily Fajardo, Edward C. Banico, Nyzar Mabeth O. Odchimar, Fredmoore L. Orosco

“…The physicochemical properties of the final construct were evaluated, and docking analyses were done with Toll-like receptors (TLRs) 3, 4, and 7 to evaluate binding affinity. A molecular dynamics simulation was then performed to determine binding stability, while immune simulations evaluated host’s immune response. …”
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Insight into Anticorrosion Mechanism of Ampicillin on Mild Steel in Acidic Environment: A Combined Experimental and Theoretical Approach by Tuan Dinh, Nguyen Minh Thong, Dinh Quy Huong, Trinh Le Huyen, Tran Duc Manh, Phan Tu Quy, Tran Xuan Mau, Pham Cam Nam

“…Moreover, Monte Carlo and molecular dynamics simulations were used to analyze the absorption behavior of inhibitor on the surface of Fe(110), which supplies the mechanism of inhibition corrosion processes. …”
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Multipotent Effect of Clozapine on Lipopolysaccharide-Induced Acetylcholinesterase, Cyclooxygenase-2,5-Lipoxygenase, and Caspase-3: In Vivo and Molecular Modeling Studies by Minhajul Arfeen, Devendra Kumar Dhaked, Vasudevan Mani

“…Further, the results from molecular docking were validated using molecular dynamics simulation (MDS) studies, confirming the results from molecular docking. …”
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Effective anti-inflammatory phenolic compounds from dandelion: identification and mechanistic insights using UHPLC-ESI-MS/MS, fluorescence quenching and anisotropy, molecular docki... by Hui Zou, Tingting Ben, Ping Wu, Geoffrey I.N. Waterhouse, Yilun Chen

“…This novel study identifies the effective anti-inflammatory phenolic compounds in dandelion and provides mechanistic insights into their interactions with receptor proteins (toll‐like receptor 4, TLR4; co‐receptor myeloid differentiation protein-2, MD-2) using UHPLC-ESI-MS/MS, lipopolysaccharide (LPS)-stimulated THP-1 cell line, fluorescence quenching and anisotropy, molecular docking (single ligand and multi-ligand docking) and molecular dynamics simulation. A 50 % aqueous methanol extract had a greater anti-inflammatory effect and higher chicoric acid content, compared with the 100 % water and 100 % methanol extracts. …”
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Networking Salt Inducible Kinase 1 Regulatory Perturbations on Type 2 Diabetes- Breast Cancer Co-Morbidity Associated Molecular Bridge by Durrani I.A., John P., Bhatti A.

“…Prospective studies on potentiating these hub genes particularly TP53, in context to SIK1 molecular dynamics may provide further insights into the molecular links tying T2DM to BC.…”
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Investigating the functional and structural effect of non-synonymous single nucleotide polymorphisms in the cytotoxic T-lymphocyte antigen-4 gene: An in-silico study. by Md Mostafa Kamal, Kazi Fahmida Haque Shantanu, Shamiha Tabassum Teeya, Md Motiar Rahman, A K M Munzurul Hasan, Douglas P Chivers, Tanveer A Wani, Atekah Hazzaa Alshammari, Mahesh Rachamalla, Francisco Carlos da Silva Junior, Md Munnaf Hossen

“…Thus, uncovering the molecular dynamics of single nucleotide polymorphisms (SNPs) within the CTLA4 gene is critical. …”
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Molecular simulation study of CO2 and O2 adsorption characteristics and diffusion pattern in coal body at atmospheric pressure by JIA Tinggui, WU Xingyu, QU Guona

“…In order to investigate the adsorption characteristics and diffusion law of CO2 and O2 in coal, the adsorption and diffusion processes of CO2 and O2 in coal at different molar ratios, temperatures and pressures were simulated using the grand canonical system Monte Carlo and molecular dynamics methods. The findings indicated that: ① CO2 was distributed in clustered aggregation and O2 was distributed in point-like dispersion in coal. …”
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The future of plant lectinology: Advanced technologies and computational tools by Vinicius J.S. Osterne, Kyria S. Nascimento, Benildo S. Cavada, Els J.M. Van Damme

“…Additionally, computational methods—including molecular docking, molecular dynamics simulations, and machine learning pipelines—support predictions of lectin structures and binding properties, underpinning experimental efforts. …”
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