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Molecular Dynamics Inc and molecular dynamics simulation program amber18
And Molecular Dynamics Simulation Program Amber18, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/molecular+simulation+program/amber18/pmc12268426-83-33-31
Average 90 stars, based on 1 article reviews
and molecular dynamics simulation program amber18 - by Bioz Stars, 2026-10
90/100 stars

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Article Title: Mechanism of palytoxin-induced ferroptosis in HaCaT cells via targeting TrxR1.
Article Snippet: .. Molecular dynamics simulation of PLTX was performed using GROMACS software to obtain its most stable conformation for subsequent docking. ..

Article Title: Structure-coevolution dual-guided engineering of C-glycosyltransferase enables high-level biosynthesis of vitexin in Yarrowia lipolytica
Article Snippet: .. Molecular dynamics simulations were performed using the AMBER 24 software package. ..

Article Title: Resveratrol suppresses GATA4/Sortilin pathway to attenuate vascular smooth muscle cell senescence-associated secretory phenotype and vascular aging-related atherosclerosis.
Article Snippet: This study aimed to investigate the role of Sortilin in vascular smooth muscle cell (VSMC) senescence and the senescence-associated secretory phenotype (SASP) and to explore whether GATA4 promotes VSMC senescence and aortic atherosclerosis by transcriptionally regulating Sortilin.. Furthermore, we examined the potential of resveratrol (Res) to alleviate vascular aging and atherogenesis via the GATA4/Sortilin pathway.. Bioinformatics analysis and experimental validation revealed co-upregulation of GATA4 and Sortilin in senescent VSMCs.

Article Title: Rational Engineering of a GH18 Chitinase for Enhanced Thermostability and Catalytic Efficiency via Dynamic Allosteric Modulation.
Article Snippet: Engineering chitinases with simultaneous improvements in catalytic efficiency and thermostability remains challenging.. Here, we present a computational strategy targeting the insertion domain (CID), a noncatalytic auxiliary region.. Using CaChi18A_ΔChBDs as the starting scaffold, folding free energy calculations identified a stabilizing mutation, A347P, within the CID hydrophobic core, which significantly enhanced thermostability by extending the half-life at 45 °C by 56 min. Based on this stabilized scaffold, evolutionary coupling analysis and stability predictions guided the design of secondary mutations, yielding several double mutants with improved catalytic performance.

Article Title: Supramolecular strategy for compartment pathogen clearance and immuno-metabolic homeostasis to treat periodontitis.
Article Snippet: .. Molecular dynamics simulations were performed using GROMACS 2021.7 software. ..

Article Title: Ditan Decoction alleviates glutamate excitotoxicity in an Aβ-induced Alzheimer's disease-like model through the regulation of ERBB2/PI3K/AKT signaling pathway.
Article Snippet: 25 Ethnopharmacological relevance: Alzheimer's disease (AD), as the most prevalent 26 form of dementia among the elders, poses a major global health challenge.. Ditan 27 Decoction (DTD), a classic prescription from traditional Chinese medicine, 28 demonstrates potent capacity against neurological disorders.. Nevertheless, the specific 29 components of DTD and its mechanisms in treating AD remain unclear.

Article Title: Multiscale Analysis of the Impact of the Isomerization of 4-Amine Tetraortho-Azobenzenes on the Structure and Dynamics of Tubular Micelles.
Article Snippet: .. Molecular dynamics (MD) simulations were performed using the GROMACS 2019 software package, employing the GROMOS 54a7 force field to model interatomic interactions.20,21 Prior to production, all systems underwent energy minimization using the steepest descent algorithm, followed by equilibration under NVT and subsequently NPT conditions for 2 ns each. ..

Article Title: In situ continuous evolution of native transporter HGT1 unlocks xylose utilization in Kluyveromyces lactis
Article Snippet: .. Molecular dynamics (MD) simulations were conducted using the GROMACS [ ] 2024.3 software package with the Amberff14sb force field, and the solvent environment was described by the TIP3P water model. ..

Molecular Dynamics Simulation:

Article Title: Structure-coevolution dual-guided engineering of C-glycosyltransferase enables high-level biosynthesis of vitexin in Yarrowia lipolytica
Article Snippet: .. Molecular dynamics simulations were performed using the AMBER 24 software package. ..

Derivative Assay:

Article Title: Ditan Decoction alleviates glutamate excitotoxicity in an Aβ-induced Alzheimer's disease-like model through the regulation of ERBB2/PI3K/AKT signaling pathway.
Article Snippet: 25 Ethnopharmacological relevance: Alzheimer's disease (AD), as the most prevalent 26 form of dementia among the elders, poses a major global health challenge.. Ditan 27 Decoction (DTD), a classic prescription from traditional Chinese medicine, 28 demonstrates potent capacity against neurological disorders.. Nevertheless, the specific 29 components of DTD and its mechanisms in treating AD remain unclear.

Solvent:

Article Title: In situ continuous evolution of native transporter HGT1 unlocks xylose utilization in Kluyveromyces lactis
Article Snippet: .. Molecular dynamics (MD) simulations were conducted using the GROMACS [ ] 2024.3 software package with the Amberff14sb force field, and the solvent environment was described by the TIP3P water model. ..



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