Martini compatible coarse-grained model of polyethylenimine for pulmonary gene delivery by Graham Lunt, Niloofar Hashemi, Subhamoy Mahajan, Tian Tang

“…Large-scale coarse-grained (CG) molecular dynamics simulations would facilitate the screening of gene carriers and understanding of the molecular mechanisms involved in pulmonary delivery. …”
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Cholesterol Induces Uneven Curvature of Asymmetric Lipid Bilayers by S. O. Yesylevskyy, A. P. Demchenko, S. Kraszewski, C. Ramseyer

“…The distribution of cholesterol in the highly curved asymmetric DOPC/DOPS lipid bilayer was investigated by the coarse-grained molecular dynamics simulations in the membrane patches with large aspect ratio. …”
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Role of Glass Composition on Mechanical Properties of Shape Memory Alloy-Metallic Glass Composites by Supat Chupradit, Indah Raya, Dinh Tran Ngoc Huy, Dmitry Bokov, Pham Van Tuan, Aravindhan Surendar, Doaa Alaa Lafta, Mustafa M. Kadhim, Olga Kravchenko, Yasser Fakri Mustafa, Zaid Hameed Mahmood, Sami Sajjadifar

“…In this work, the molecular dynamics (MD) simulation was applied to design a laminated composite structure comprised of the shape memory alloy (SMA) and Cu-Zr metallic glasses (MGs). …”
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Spontaneous curvature in two-dimensional van der Waals heterostructures by Yuxiang Gao, Fenglin Deng, Ri He, Zhicheng Zhong

“…Based on deep-learning-assisted large-scale molecular dynamics simulations, we observe significant out-of-plane displacements up to 3.8 Å in graphene/BN bilayers induced by curvature, producing a stable hexagonal moiré pattern, which agrees well with experimentally observations. …”
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Machine Learning-Assisted Drug Repurposing Framework for Discovery of Aurora Kinase B Inhibitors by George Nicolae Daniel Ion, George Mihai Nitulescu, Dragos Paul Mihai

“…<b>Methods:</b> This study introduces a machine learning-assisted drug repurposing framework integrating quantitative structure-activity relationship (QSAR) modeling, molecular fingerprints-based classification, molecular docking, and molecular dynamics (MD) simulations. Using this pipeline, we analyzed 4680 investigational and approved drugs from DrugBank database. …”
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Understanding Rifampicin Resistance in Tuberculosis through a Computational Approach by Satish Kumar, Lingaraja Jena

“…Subsequently, this was verified by molecular dynamics simulations. This in silico evidence may help us understand RIF resistance in rpoB mutant strains.…”
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Plants and fungi metabolites as novel autophagy inducers and senescence inhibitors by Rivka Ofir

“…New AI/SI can be identified using various approaches like hypothesis-driven approach for screening receptor agonists using an in-silico library of thousands of natural compounds; cheminformatics studies of phytochemicals using docking and molecular dynamics simulation, structure similarities/mimicry in vitro, “blind” high throughput screening (HTS) of libraries of natural metabolites against relevant models, and more. …”
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Unzipping of knotted DNA via nanopore translocation by Antonio Suma, Cristian Micheletti

“…DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA–enzyme interactions in biological systems. Here we use molecular dynamics simulations and a coarse-grained model of DNA to address the nanopore unzipping of DNA filaments that are knotted. …”
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A MD Simulation and Analysis for Aggregation Behaviors of Nanoscale Zero-Valent Iron Particles in Water via MS by Ying Zhao, Dongmei Liu, Huan Tang, Jing Lu, Fuyi Cui

“…NZVI are used widely in many fields resulting in more NZVI in water environment. Molecular dynamics simulations and Materials Studio software are used to investigate the microaggregation behaviors of NZVI particles. …”
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Molecular surface descriptors to predict antibody developability: sensitivity to parameters, structure models, and conformational sampling by Eliott Park, Saeed Izadi

“…Averaging the descriptor values over conformational distributions from molecular dynamics mitigates the systematic shifts and improves the consistency across different structure prediction methods, albeit with inconsistent improvements in correlations with biophysical data. …”
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Linking machine learning and biophysical structural features in drug discovery by Armin Ahmadi, Shivangi Gupta, Vineetha Menon, Jerome Baudry

“…IntroductionMachine learning methods were applied to analyze pharmacophore features derived from four protein-binding sites, aiming to identify key features associated with ligand-specific protein conformations.MethodsUsing molecular dynamics simulations, we generated an ensemble of protein conformations to capture the dynamic nature of their binding sites. …”
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Leiomodin creates a leaky cap at the pointed end of actin-thin filaments. by Dmitri Tolkatchev, Garry E Smith, Lauren E Schultz, Mert Colpan, Gregory L Helms, John R Cort, Carol C Gregorio, Alla S Kostyukova

“…Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first atomic structural model of the binding interface between the tropomyosin-binding site of cardiac leiomodin and the N-terminus of striated muscle tropomyosin. …”
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In Silico Study of Alkaloids: Neferine and Berbamine Potentially Inhibit the SARS-CoV-2 RNA-Dependent RNA Polymerase by Rishab Marahatha, Asmita Shrestha, Kabita Sharma, Bishnu P. Regmi, Khaga Raj Sharma, Pramod Poudel, Ram Chandra Basnyat, Niranjan Parajuli

“…Among the different alkaloids studied, neferine and berbamine were repurposed as potential drug candidates based on their binding affinity and interactions with RdRP. Further, molecular dynamics simulation of 90 ns revealed the conformational stability of the neferine-RdRP complex.…”
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Adsorption of Phenols from Different Solvents on Graphene: Semi-Empirical Quantum Mechanical Calculations by Pablo Húmpola, Héctor S. Odetti, Alberto G. Albesa, José L. Vicente

“…The adsorption of phenol from aqueous solutions on carbon surfaces is discussed from different theoretical points of view, such as Monte–Carlo simulations, semi-empirical calculations, density functional theory and molecular dynamics. We performed a quantitative analysis of the adsorption of aromatics in general, and phenolic compounds in particular, through semi-empirical quantum mechanical calculations using different approaches. …”
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The Stability of a Model Substrate for Topoisomerase 1-Mediated DNA Religation Depends on the Presence of Mismatched Base Pairs by William H. Gmeiner, Freddie Salsbury, Chris M. Olsen, Luis A. Marky

“…In the present study, we report that mismatched base pairs at the +1 position destabilize the duplex DNA components for a model Top1 cleavage complex formation even though one duplex component does not directly include a mismatched base pair. Molecular dynamics simulations reveal G-dU and G-FdU mismatched base pairs, but not a G-T mismatched base pair, increase flexibility at the Top1 cleavage site, and affect coupling between the regions required for the religation reaction to occur. …”
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Spermine Significantly Increases the Transfection Efficiency of Cationic Polymeric Gene Vectors by Yue Lv, Jiaoqin Xue, Pengfei Cui, Lin Qiu

“…Characterization of PEI/Spermine/DNA revealed that, compared to PEI/DNA, its particle size increased to approximately 150 nm. Molecular dynamics simulation results revealed that spermine can enhance the interaction between PEI and DNA, thereby forming a system with lower energy and greater stability. …”
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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

“…The top two candidates, AZD3839 and LY2090314, were selected for molecular dynamics simulation studies over 100 ns to assess binding stability. …”
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Exosomal circRNAs: Deciphering the novel drug resistance roles in cancer therapy by Xi Li, Hanzhe Liu, Peiyu Xing, Tian Li, Yi Fang, Shuang Chen, Siyuan Dong

“…Their presence in bodily fluids positions them as potential non-invasive biomarkers, revealing the molecular dynamics of cancers. Research in exosomal circRNAs is reshaping our understanding of neoplastic intercellular communication. …”
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Amentoflavone from Selaginella bryopteris leaf extracts modulate MAPK signaling - Molecular modeling study for therapeutic target analysis by Praveen Mallari, Mashooq Ahmad Bhat

“…Interaction networks were built for the corresponding proteins, molecular docking, molecular dynamics, and molecular mechanics. Poisson–Boltzmann surface area (MMPBSA) binding free energy calculations were performed. …”
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Curcumin mimics of potential chemoprevention with NQO1 induction properties by Dalia R. Aboshouk, Ahmed R. Hamed, Siva S. Panda, Mohamed S. Bekheit, M. Adel Youssef, Adel S. Girgis

“…Molecular modeling studies (including QSAR, molecular docking and molecular dynamics) were accessed supporting the observed biological profiles.…”
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