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Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
BackgroundThe molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures. The molecular...
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Identification of potential FAK inhibitors using mol2vec molecular descriptor-based QSAR, molecular docking, ADMET study, and molecular dynamics simulation
This study aims to identify potential focal adhesion kinase (FAK) inhibitors through an integrated computational approach, combining mol2vec...
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Molecular Dynamics Simulation Methods to Study Structural Dynamics of Proteins
Molecular dynamics (MD) simulation is a computational technique for understanding the physical motions of atomic and molecular particles. In this...
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Network pharmacology, molecular docking, and molecular dynamics simulation analysis reveal the molecular mechanism of halociline against gastric cancer
Halociline, a derivative of alkaloids, was isolated from the marine fungus Penicillium griseofulvum by our group. This remarkable compound exhibits...
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Molecular Dynamics Simulation and Docking of MUC1 O-Glycopeptide
Advances in computer performance and computational simulations allow increasing sophistication in applications in biological systems. Molecular...
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Molecular Dynamics Simulations
Molecular simulations aim to supplement the design of new peptide molecules and the prediction of their conformational landscape. The response of...
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Protein-Protein Interaction Studies Using Molecular Dynamics Simulation
Protein-protein interactionProtein-protein interaction (PPI) is a crucial event for many biological functions. Studying the molecular details of PPI...
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Molecular Dynamics Simulation of Permeation Through Connexin Channels
Molecular dynamics (MD) simulations are a collection of computational tools that can be used to trace intermolecular interactions at the...
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Towards new bioactive fluorine-containing 1,3,4-oxadiazole-amide derivatives: synthesis, antibacterial activity, molecular docking and molecular dynamics simulation study
Through the approach of molecular hybridization, this study rationally designed and synthesized new trifluoromethyl-1,3,4-oxadiazole amide...
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Study of Glabranin as an Inhibitor Against Prostate Cancer: Molecular Docking, Molecular Dynamics Simulation, MM-PBSA Calculation and QSAR Prediction
Prostate cancer is the World's second most frequent malignancy, with the fifth-highest male mortality rate. In advanced prostate cancer patients,...
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Repurposing FDA approved drugs against monkeypox virus DNA dependent RNA polymerase: virtual screening, normal mode analysis and molecular dynamics simulation studies
Zoonotic monkeypox disease, caused by the double-stranded DNA monkeypox virus, has become a global concern. Due to the absence of a specific small...
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Network pharmacology, molecular docking, and molecular dynamics simulation to elucidate the mechanism of anti-aging action of Tinospora cordifolia
Scientific research has demonstrated that Tinospora cordifolia acts as an anti-aging agent in several experimental models, generating global interest...
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Molecular Dynamics Simulation to Study Thermal Unfolding in Proteins
The proper folding of a protein is essential for its biological functions. Thermal denaturation of protein structure has been used as an essential...
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Identification of phytocompounds from Paris polyphylla Smith as potential inhibitors for HER2 & VEGFR2 cancer genes using molecular docking and molecular dynamics simulation studies
In the present studies, molecular docking and molecular dynamic simulation analyses were done to identify phytocompounds from Paris polyphylla as...
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Inhibition of Monkeypox Virus DNA Polymerase Using Moringa oleifera Phytochemicals: Computational Studies of Drug-Likeness, Molecular Docking, Molecular Dynamics Simulation and Density Functional Theory
The emergence of zoonotic monkeypox (MPX) disease, caused by the double-stranded DNA monkeypox virus (MPXV), has become a global threat. Due to...
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Discovery of Palbociclib as a potent c-Myc G4 stabilizer for lung cancer treatment using molecular docking, molecular dynamics simulation, and in vitro activity evaluation
Despite significant progress in lung cancer treatment, this disease remains a prevalent and serious global malignancy, leading to high rates of...
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Identifying β-secretase 1 (BACE1) inhibitors from plant-based compounds: an approach targeting Alzheimer’s therapeutics employing molecular docking and dynamics simulation
β-secretase 1 (BACE1) is an enzyme that is involved in generating beta-amyloid peptides and is believed to have a significant role in the development...
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Molecular Dynamics Simulation to Study Protein Conformation and Ligand Interaction
The field of molecular dynamics (MD) simulations has become indispensable today to studying the conformational flexibility and dynamics of proteins...
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Molecular Dynamics Simulation of the Conformational Mobility of the Lipid-Binding Site in the Apolipoprotein E Isoforms ε2, ε3, and ε4
AbstractNeurodegenerative disorders, particularly Alzheimer’s disease, have become a major global healthcare issue. Despite extensive research, the...
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Unraveling the anti-breast cancer activity of Cimicifugae rhizoma using biological network pathways and molecular dynamics simulation
Cimicifugae is a commonly used treatment for breast cancer, but the specific molecular mechanisms underlying its effectiveness remain unclear. In...
