Unravelling the Methylene Blue Adsorption Mechanism on Doped and Nondoped Polyaniline: A Combined Molecular Modeling and Experimental Investigation by Souad Djellali, Amani Touati, Abderrahmane Semmeq, Maya Kebaili, Michael Badawi, Adrián Bonilla-Petriciolet

“…Static DFT and DFT-based ab initio molecular dynamics were used to characterize the intermolecular interactions of this dye molecule with nondoped and doped PANI. …”
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Challenging the ideal strength limit in single-crystalline gold nanoflakes through phase engineering by Tong Zhang, Yuanbiao Tong, Chenxinyu Pan, Jun Pei, Xiaomeng Wang, Tao Liu, Binglun Yin, Pan Wang, Yang Gao, Limin Tong, Wei Yang

“…First-principles and molecular dynamics (MD) calculations demonstrate that the mechanical properties arise from the unconventional HCP structure as well as the strong surface effect. …”
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Anti-Inflammatory therapeutic potential of Bungur (Lagerstroemia speciosa L.) leaves ethanolic extract against LPS-activated macrophage through TLR4/MD2 signaling: A computational... by Rosyadah Nuraini, Dwijayanti Dinia Rizqi, Annisa Yuslinda, Kamila Fairuz Sarah, Widyananda Muhammad Hermawan, Ulfa Siti Mariyah, Widodo Nashi

“…Molecular docking and molecular dynamics simulations were conducted to evaluate the interaction and stability of selected compounds with TLR4/MD2 complex. …”
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Molecular Understanding of the Role of Catalyst Particle Arrangement in Local Mass Transport Resistance for Fuel Cells by Aoxin Ran, Linhao Fan, Chasen Tongsh, Jiaqi Wang, Zhengguo Qin, Qing Du, Meng Ni, Kui Jiao

“…Herein, using a unique method coupling Hybrid Reverse Monte Carlo, molecular dynamics simulations, and experimental measurements, a Pt particle arrangement strategy is proposed to reduce local oxygen transport resistance, based on a molecular‐level understanding of its impact. …”
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Saponins Effect on Human Insulin Amyloid Aggregation by Eleonora Mari, Silvia Vilasi, Paolo Moretti, Maria Rosalia Mangione, Giorgia Giorgini, Roberta Galeazzi, Maria Grazia Ortore

“…To deepen the understanding of the saponins interaction with insulin, a Molecular Dynamics investigation is performed, too. The reported data demonstrate that saponins interfere with the amyloid aggregation by inducing a strong inhibition on the formation of insulin fibrils, likely through specific interactions with insulin monomers. …”
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Targeting SLC4A4: A Novel Approach in Colorectal Cancer Drug Repurposing by Krunal Pawar, Pramodkumar P. Gupta, Pooran Singh Solanki, Ravi Ranjan Kumar Niraj, Shanker L. Kothari

“…Results: The study identified the compound (5R)-N-[(1r)-3-(4-hydroxyphenyl)butanoyl]-2-decanamide (DB07991) as the best ligand, demonstrating favorable binding affinity and stability. Molecular dynamics simulations revealed strong protein–ligand interactions with consistent RMSD (~0.25 nm), RMSF (~0.5 nm), compact Rg (4.0–3.9 nm), and stable SASA profiles, indicating that the SLC4A4 structure remains stable upon ligand binding. …”
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Fullerene-containing modifier of magnetoactive elastomer by М.A. Vasilyeva, F.Yu. Sharikov, I.A. Bogdanov

“…Aggregation, limited by diffusion processes, proceeds to limit the reaction rate; at the final stage, spatial limitation dominates.Studying the molecular dynamics of aggregates formation in various solutions allows improved understanding the principles of a fractal structure formation. …”
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Structural insights into light-gating of potassium-selective channelrhodopsin by Takefumi Morizumi, Kyumhyuk Kim, Hai Li, Probal Nag, Tal Dogon, Oleg A. Sineshchekov, Yumei Wang, Leonid S. Brown, Songhwan Hwang, Han Sun, Ana-Nicoleta Bondar, Igor Schapiro, Elena G. Govorunova, John L. Spudich, Oliver P. Ernst

“…This switch triggers a series of side chain reorientations and merges intramolecular cavities into a transmembrane K+ conduction pathway. Molecular dynamics simulations confirm K+ flux through the illuminated state but not through the resting state. …”
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Exploring molecular determinants and pharmacokinetic properties of IgG1-scFv bispecific antibodies by Kristina M.J. Aertker, Minu Ravindra Pilvankar, Tobias M. Prass, Michaela Blech, Fabian Higel, Srinath Kasturirangan

“…FcRn chromatography results revealed specific scFv-FcRn interactions that are unique to the IgG1-scFv, which was further supported by molecular dynamics (MD) simulation. These interactions likely stabilize the BsAb FcRn interaction at physiological pH, which in turn could disrupt FcRn-mediated BsAb recycling. …”
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Effect of titin phosphorylation on degradation of titin from skeletal muscles by Ying Wang, Xin Li, Dequan Zhang, Zheng Li, Baocai Xu, Jie Zhu

“…There were 20, 16 and 12 phosphorylated sites identified by iTRAQ in the PKA, control and AP group, respectively. 3D structure of dephosphorylated titin fragment was simulated and its molecular dynamics trajectory analysis was performed using Discovery StudioTM. …”
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Deciphering the potential of plant metabolites as insecticides against melon fly (Zeugodacus cucurbitae): Exposing control alternatives to assure food security by Zinat Jahan Chowdhury, Anik Banik, Tanjin Barketullah Robin, Mohammed Rashed Chowdhury

“…Stability of the top compound-protein complexes was further confirmed through a 100 ns molecular dynamics simulation. In insecticide-likeness evaluations, jervine consistently scored high, with camptothecin also performing well, while neriifolin ranked lower. …”
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Predicting deamidation and isomerization sites in therapeutic antibodies using structure-based in silico approaches by David Hoffmann, Joschka Bauer, Markus Kossner, Andrew Henry, Anne R. Karow-Zwick, Giuseppe Licari

“…The predictive accuracy of the model was evaluated for four different states of the protein structure: (1) static homology models, (2) enhancing low-frequency vibrational modes during short molecular dynamics (MD) runs, (3) a combination of (2) with a protonation state reassignment, and (4) conventional full-atomistic MD simulations. …”
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Gypsum heterogenous nucleation pathways regulated by surface functional groups and hydrophobicity by Yan-Fang Guan, Xiang-Yu Hong, Vasiliki Karanikola, Zhangxin Wang, Weiyi Pan, Heng-An Wu, Feng-Chao Wang, Han-Qing Yu, Menachem Elimelech

“…Results based on classical nucleation theory and molecular dynamics simulations reveal that nucleation pathways for hydrophilic surfaces involve surface-induced nucleation, with ion adsorption sites (i.e., functional groups) serving as anchors to facilitate the growth of vertically oriented clusters. …”
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4,6-Disubstituted pyrimidine-based microtubule affinity-regulating kinase 4 (MARK4) inhibitors: synthesis, characterization, in-vitro activity and in-silico studies by Ashanul Haque, Khalaf M. Alenezi, Mohd. Saeed Maulana Abdul Rasheed, Md. Ataur Rahman, Saleha Anwar, Shahzaib Ahamad, Dinesh Gupta

“…Molecular docking and molecular dynamics (MD) simulation at 500 ns was carried out against MARK4 (PDB: 5ES1). …”
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Design and In Silico and In Vitro Evaluations of a Novel Nicotinamide Derivative as a VEGFR-2 Inhibitor by Ibrahim H. Eissa, Muhammad Abd ElGayed Bkrah, Reda G. Yousef, Hazem Elkady, Eslam B. Elkaeed, Bshra A. Alsfouk, Ibrahim M. Ibrahim, Ahmed M. Metwaly, Dalal Z. Husein

“…Molecular docking revealed its capability to inhibit VEGFR-2, which was further supported by molecular dynamics (MD) simulations confirming its binding to the target protein. …”
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Discovery and Characterization of Two Selective Inhibitors for a Mu-Class Glutathione S-Transferase of 25 kDa from <i>Taenia solium</i> Using Computational and Bioinformatics Tools by César Sánchez-Juárez, Roberto Flores-López, Lluvia de Carolina Sánchez-Pérez, Ponciano García-Gutiérrez, Lucía Jiménez, Abraham Landa, Rafael A. Zubillaga

“…The workflow involved modeling and refining the 3D structure from the sequence using the AlphaFold algorithm and all-atom molecular dynamics simulations with an explicit solvent. …”
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Discovery of novel and highly potent small molecule inhibitors targeting FLT3-ITD for the treatment of acute myeloid leukemia using structure-based virtual screening and biological... by Kun Shi, Kun Shi, Ye Hong, Ye Hong, Ye Hong, Huajing Liu, Xiaotian Yang, Fengzhen Wang, Fengzhen Wang, Yanming Zhang

“…This potency was significantly superior to that of the known positive inhibitor Midostaurin, showing approximately 27 times higher inhibitory potency. Molecular dynamics simulations have confirmed the stable interaction between FLIN-4 and FLT3. …”
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Microbial-based natural products as potential inhibitors targeting DNA gyrase B of Mycobacterium tuberculosis: an in silico study by Tilal Elsaman, Magdi Awadalla Mohamed, Malik Suliman Mohamed, Eyman Mohamed Eltayib, Abualgasim Elgaili Abdalla

“…Notably, 1-Hydroxy-D-788-7, an anthracycline derivative, demonstrated superior binding affinity in molecular dynamics simulations. The RMSD values, ranging from 1.7 to 2.5 Å, alongside RMSF analysis and a detailed evaluation of the established interaction forces, revealed that 1-Hydroxy-D-788-7 was the strongest binder to Mycobacterial DNA Gyrase B. …”
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SARS-CoV-2 ORF3a accessory protein is a water-permeable channel that induces lysosome swelling by Antonio Michelucci, Luigi Sforna, Riccardo Focaia, Maria Vittoria Leonardi, Angela Di Battista, Giorgia Rastelli, Simone Vespa, Simona Boncompagni, Manlio Di Cristina, Luigi Catacuzzeno

“…To unravel the potential function of ORF3a, here we employed a multidisciplinary approach including patch-clamp electrophysiology, videoimaging, molecular dynamics (MD) simulations, and electron microscopy. …”
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Exploring Echinacea angustifolia for anti-viral compounds against Zika virus RNA-dependent RNA polymerase: a computational study by Mai M. El-Daly, Leena H. Bajrai, Thamir A. Alandijany, Isra M. Alsaady, Hattan S. Gattan, Meshari M. Alhamdan, Vivek Dhar Dwivedi, Esam I. Azhar

“…To assess the robustness and effectiveness of these interactions, we performed molecular dynamics simulations along with calculations of the binding free energy and PCA analysis. …”
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