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8 articles for “molecular dynamics (MD) simulations”
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Computational Simulations in Drug Discovery: Modeling Protein Folding and Drug Binding
Abstract: Computational simulations have become essential tools in drug discovery, offering unprecedented insights into molecular behavior at the atomic level. These simulations, particularly in the domains of protein folding and drug binding, allow for the exploration of complex biological systems that are often difficult to study experimentally. Protein folding, a critical aspect of drug discovery, involves the transition of a polypeptide chain from an unfolded to a biologically active structure. Understanding …
Published in Research and Reviews : Journal of Computational Biology · Vol. 14, Issue 1, 2025 · pp. 23–29 Read article
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Computational Biomodeling: Transforming Drug Design with Advanced Simulations
Abstract: Computational biomodeling has emerged as a transformative approach in the field of drug discovery, significantly enhancing the efficiency and precision of identifying and optimizing potential drug candidates. This article explores the various computational techniques utilized in drug design, including molecular docking, molecular dynamics (MD) simulations, free energy calculations, and virtual screening, and examines how these methods collectively contribute to the drug development process. The integration of these advanced simulations allows …
Published in Research and Reviews : Journal of Computational Biology · Vol. 13, Issue 3, 2024 · pp. 24–29 Read article
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Advanced Computational Models for Predicting Molecular Interactions
Abstract: Understanding molecular interactions is essential for a number of disciplines, including biochemistry, materials science, and medication development. Traditional experimental methods, while accurate, are often time-consuming and expensive. Advanced computational models have emerged as powerful tools to predict molecular interactions efficiently. In order to predict the behavior and interactions of molecules at the atomic and subatomic levels, this paper reviews the most recent developments in computational techniques, such as machine learning …
Published in International Journal of Advance in Molecular Engineering · Vol. 2, Issue 1, 2024 · pp. 8–13 Read article
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Overview of Ionic Polarization: A Model Based Novel Approach
Abstract: This study presents a comprehensive analysis of ionic polarization through a novel model-based approach that integrates theoretical, computational, and experimental methodologies. Ionic polarization, which significantly influences the dielectric properties of materials, is examined through the lens of the Clausius-Mossotti equation and the Debye relaxation model, providing a theoretical framework for understanding the relationship between ionic displacement and dielectric behavior. To explore ionic displacement and polarization at the atomic level, advanced …
Published in International Journal of Cheminformatics · Vol. 2, Issue 2, 2024 · pp. 18–25 Read article
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Crystal Defects and Their Characterization in Modern Materials Science
Abstract: The physical and chemical properties of crystalline solids are fundamentally dictated by deviations from structural perfection, known as crystal defects. From the point-scale vacancies that drive diffusion to the planar boundaries that determine mechanical strength, defects serve as the primary "tuning knobs" in material design. This review provides a comprehensive examination of point, line, and planar defects, exploring their formation energetics and their role in plastic deformation via crystallographic slip. …
Published in International Journal of Crystalline Materials · Vol. 3, Issue 1, 2026 · pp. 15–19 Read article
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Exploration of Diverse Epoxy-Based Surface Coating Methods for Enhancing Anticorrosion Characteristics
Abstract: Epoxy-based polymers, commonly referred to as polyepoxides, constitute one of the most versatile and widely adopted categories of polymeric materials due to their exceptional structural, mechanical, and chemical characteristics. Their unique macromolecular framework enables strong interfacial bonding, high mechanical stability, and superior resistance to environmental and chemical degradation, positioning them as advanced alternatives to many traditional organic corrosion inhibitors that often fail under prolonged exposure to aggressive conditions When polyepoxides …
Published in Journal of Polymer & Composites · Vol. 14, Issue 2, 2026 · pp. 167–177 Read article
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Exploring the Role of MAPK3 in Major Depressive Disorder: Molecular Docking, Dynamics, and Binding Free Energy Analysis of Natural Compounds as Alternatives to Conventional Drugs
Abstract: Major Depressive Disorder (MDD) is a prevalent neuropsychiatric disorder with limited treatment efficacy and significant side effects associated with conventional antidepressants. Recent studies have highlighted the role of mitogen-activated protein kinase 3 (MAPK3) in the mechanisms underlying MDD, positioning it as a potential target for the development of novel therapeutic drugs. In this study, we employed various computational approaches to explore natural compounds as viable alternatives to synthetic antidepressants. Researchers …
Published in International Journal of Bioinformatics and Computational Biology · Vol. 3, Issue 2, 2025 · pp. 53–68 Read article
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Modulating Immune System of Mosquitoes with A Novel Salicylate Derivative: A Bioinformatics-Based Study
Abstract: The present study aims to compare the interactions of a novel derivative of salicylic acid, 5-(2-nitroethynl) salicylic acid (5-SANA, salicylic acid nitroalkene), and salicylic acid with the critical residues of mosquito’s juvenile hormone binding protein (mJHBP). Given the better water solubility of 5-SANA and salicylic acid, it is believed that they can interact quicker than the natural substrate, juvenile hormone (JH), with the cavity of mJHBP, a circulating protein in …
Published in Research and Reviews : A Journal of Immunology · Vol. 16, Issue 1, 2026 · pp. 1–5 Read article