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32 articles for “molecular dynamics simulation”
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Analysis of Bioinformatics Software Applied in Computer-Aided Drug Design
Abstract: The integration of bioinformatic tools with computational methods has revolutionized the field of Computer-aided Drug Design (CADD), enabling researchers to expedite the discovery and optimization of new therapeutics. This review provides an in-depth analysis of the bioinformatic tools utilized in CADD, encompassing molecular docking, molecular dynamics simulation, virtual screening, homology modelling, and molecular visualization. We go over the tenets, approaches, and uses of these instruments, emphasizing their value in expediting …
Published in Research & Reviews: A Journal of Drug Design & Discovery · Vol. 11, Issue 2, 2024 · pp. 1–10 Read article
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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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A Review of Drug Design Techniques Assisted by Computers to Combat Diabetes
Abstract: Diabetes mellitus is a global health concern characterized by chronic hyperglycemia and associated complications. The creation of innovative medicines with enhanced efficacy and safety profiles continues to be a top focus, notwithstanding improvements in treatment. A useful method in drug development, computer-aided drug design (CADD) makes it easier to identify possible therapeutic candidates and optimise lead molecules. An extensive synopsis of CADD tactics used in the fight against diabetes is …
Published in Emerging Trends in Personalized Medicines · Vol. 2, Issue 1, 2025 · pp. 1–10 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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Advancements in Molecular Engineering: Innovations at the Nexus of Chemistry and Technology
Abstract: Molecular engineering, a frontier of chemistry, merges precision and innovation to design and assemble molecular structures with unprecedented control. This abstract explores recent advances, highlighting key breakthroughs and their transformative impacts. Starting with its roots in chemical synthesis and materials science, it traces the evolution towards rational design driven by computational tools and advanced characterization techniques, enabling tailored molecular architectures. A focal point is programmable molecules, where DNA nanotechnology principles …
Published in International Journal of Advance in Molecular Engineering · Vol. 1, Issue 2, 2023 · pp. 37–43 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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Modern Computer-aided Drug Design Methods: A Review
Abstract: Computer-aided drug design (CADD) has emerged as a crucial tool in the drug discovery process, offering a time-efficient and cost-effective approach to identifying potential drug candidates. This review aims to provide an overview of modern CADD methods, including high-throughput screening (HTS), structure-based drug design (SBDD), ligand-based drug design (LBDD), structure-based virtual screening (SBVS), and ligand-based virtual screening (LBVS). We discuss the basic principles, applicability, and limitations of each method, highlighting …
Published in Research and Reviews: A Journal of Dentistry · Vol. 15, Issue 2, 2024 · pp. 14–20 Read article
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Samelisant, an H3 Receptor Agonist as an Anti-Alzheimer Potential – A Pilot Study on Molecular Docking
Abstract: Neurodegenerative diseases have become more prevalent and about 55 million of the population are affected by dementia globally. One of the most important neurodegenerative diseases is Alzheimer’s disease which is known for its effect on memory and cognitive impairment. Alzheimer’s disease (AD) is an area of intense scientific investigation due to its high prevalence and the lack of a definitive cure. Amyloid precursor protein plays a central role in Alzheimer’s …
Published in International Journal of Brain Sciences · Vol. 3, Issue 1, 2026 · pp. 15–26 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
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Enzyme Stability Prediction using BERT and CNN-A Deep Learning Approach for Enhanced Biocatalysis
Abstract: An important factor in determining the efficacy of industrial enzymes used in various biotechnological applications is their stability. The goal of this study is to develop a predictive model for industrial enzyme stability, which is essential to the efficiency of these enzymes in biotechnological applications. The research takes a comprehensive strategy to comprehend the parameters affecting enzyme stability by combining statistical analysis, deep learning algorithms (BERT and CNN), and molecular …
Published in Research and Reviews : A Journal of Life Sciences · Vol. 14, Issue 2, 2024 · pp. 19–35 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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Computational Approaches to Understanding Cellular Signaling Pathways
Abstract: Cellular signaling pathways are fundamental in regulating vital processes, such as cell growth, differentiation, and apoptosis. The intricate and interconnected nature of these signaling networks requires sophisticated methods for their analysis. Computational approaches, including mathematical modeling, network analysis, and machine learning, have revolutionized the way researchers analyze and simulate cellular signaling. This article provides a comprehensive overview of computational strategies employed to model signaling pathways, with a focus on integrating …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 2, Issue 2, 2024 · pp. 8–13 Read article
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Crystal Engineering Strategies for Tailoring Mechanical Properties of Structural Materials
Abstract: Crystal engineering has emerged as a promising approach for designing materials with tailored mechanical properties, enabling advancements in various fields such as aerospace, automotive, and construction. This review examines the diverse strategies employed in crystal engineering to manipulate the mechanical behavior of structural materials. One key strategy involves controlling the crystal structure at the atomic level through techniques such as alloying, doping, and phase transformations. Alloying introduces foreign atoms into …
Published in International Journal of Crystalline Materials · Vol. 1, Issue 1, 2024 · pp. 01–06 Read article
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Computational Exploration of Aristolochia indica Bioactive Compounds Against Snake Venom Proteins Using Docking and Dynamics Simulations
Abstract: Snakebite envenoming is a neglected health threat impacting millions of people each year especially in tropical and subtropical countries. Ethnomedicinal plants are sources of various bioactive compounds and have been utilised by several tribes across the world for centuries. Aristolochia indica is a perennial herb mentioned in the Indian Ayurveda with a long history of use against snake venom, scorpion venom, fevers, rheumatic arthritis, liver ailments, leishmaniasis etc. The major …
Published in Research and Reviews : Journal of Computational Biology · Vol. 15, Issue 1, 2026 Read article
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Computational Modeling of Polymer Semiconductors for Electronic Applications
Abstract: Polymer semiconductors have become important materials in modern electronic applications because they combine semiconducting behavior with mechanical flexibility, low-cost processing, and tunable molecular structure. Their growing use in organic field-effect transistors, organic photovoltaics, organic light-emitting diodes, and flexible sensing devices has increased the need for accurate computational approaches that can predict material properties and device performance before experimental fabrication. This paper reviews the major computational modeling techniques used for polymer …
Published in Journal of Polymer & Composites · Vol. 14, Issue 3, 2026 · pp. 132–146 Read article
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Advancements in Drug Design Technology and Its Impact on COVID-19 Treatment
Abstract: The deadly coronavirus disease 19 (COVID-19) pandemic has recently spread, raising concerns about global health. The search for novel therapeutic compounds is made more necessary by the persistent problem of the absence of licensed medications or vaccinations. By saving money and time, computer-aided drug design has sped up the process of finding and developing new drugs. The structured-based and ligand-based drug discovery subcategories of computer-aided drug design (CADD) are the …
Published in International Journal of Virus Studies · Vol. 1, Issue 1, 2024 · pp. 1–15 Read article
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Effectiveness of PTFE-Based Nano-coatings in Improving Corrosion and Wear Resistance of Stainless Steel
Abstract: Polytetrafluoroethylene (PTFE) has emerged as a highly effective material for enhancing the durability and performance of metal surfaces, particularly in environments requiring superior corrosion resistance and low friction. This study investigates the application of PTFE coatings on various metallic substrates, with a focus on stainless steel and carbon steel, to improve their corrosion resistance, wear protection, and tribological performance. Utilizing advanced deposition techniques such as sol-gel and plasma spray, PTFE …
Published in International Journal of Photochemistry and Photochemical Research · Vol. 2, Issue 2, 2024 · pp. 32–38 Read article
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Interaction of Mosquito’s hppd Enzyme with Lansoprazole Sulfide A New Hope to Tackle the Mosquito Menace – an in-Silico Study
Abstract: Tyrosine detoxification is an important physiological process that helps blood-feeding insects, such as mosquitoes that transmit Plasmodium parasites causing malaria, digest their blood meals. An enzyme known as 4-hydroxyphenylpyruvate dioxygenase (HPPD), which is part of the tyrosine detoxification pathway, helps in removing excess tyrosine in a high-protein blood meal. Excess tyrosine can be lethal to the insects, and hence, the role of HPPD enzyme is very critical. Inhibitors of HPPD …
Published in International Journal of Insects · Vol. 3, Issue 1, 2026 · pp. 1–11 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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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