Using Molecular Dynamics Free Energy Simulation to Compute Binding Affinities of DNA G-Quadruplex Ligands.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-9666-7_10
Abstract: We provide a practical guide for using molecular dynamics simulation to compute the binding affinity of small molecules in complex with G-quadruplex DNA. Such calculations have a number of applications, such as rescoring docking results… read more here.
Keywords: molecular dynamics; energy; simulation compute; using molecular ... See more keywords
Effect of magnesium sulfate in oxidized lipid bilayers properties by using molecular dynamics
Sign Up to like & getrecommendations! Published in 2021 at "Biochemistry and Biophysics Reports"
DOI: 10.1016/j.bbrep.2021.100998
Abstract: Magnesium sulfate (MgSO4) has been used as a protector agent for many diseases related to oxidative stress. The effect of MgSO4 on the oxidized lipid bilayer has not yet been studied using molecular dynamics calculations.… read more here.
Keywords: oxidation; molecular dynamics; using molecular; magnesium sulfate ... See more keywords
Surfactant pKa Calculations using Molecular Dynamics Simulations
Sign Up to like & getrecommendations! Published in 2017 at "Biophysical Journal"
DOI: 10.1016/j.bpj.2016.11.2821
Abstract: The protonation state for ionizable surfactants is crucial for self-assembly, phase behavior, and morphology. For example, oleic acid forms vesicles at intermediate pH conditions (∼7-9), micelles at high pH, and oil phases at low pH.… read more here.
Keywords: molecular dynamics; using molecular; surfactant pka; pka calculations ... See more keywords
Investigating local atomic structural order in TiAl3 metallic glass using molecular dynamic simulation
Sign Up to like & getrecommendations! Published in 2018 at "Computational Condensed Matter"
DOI: 10.1016/j.cocom.2018.01.005
Abstract: Abstract In this work, we studied structural properties of super cooled binary TiAl3 metallic glass (MG) using molecular dynamics (MD) simulation in the framework of embedded atom method (EAM). The atomic local structure is analyzed… read more here.
Keywords: metallic glass; tial3 metallic; glass using; glass ... See more keywords
Quantifying the rejuvenation effects of soybean-oil on aged asphalt-binder using molecular dynamics simulations
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Cleaner Production"
DOI: 10.1016/j.jclepro.2021.128375
Abstract: Abstract Aging is responsible for the irreversible asphalt-binder stiffening and brittleness. However, various rejuvenators can recycle the aged asphalt-binder. In this study, molecular models of rejuvenators for aged asphalt-binders were constructed using molecular dynamic (MD)… read more here.
Keywords: using molecular; soybean oil; aged asphalt; asphalt binder ... See more keywords
Modeling the thermal poling of glasses using molecular dynamics. Part 1: Effects on glass structure
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Non-crystalline Solids"
DOI: 10.1016/j.jnoncrysol.2017.01.045
Abstract: Abstract Due to its ability to permanently alter key properties of glasses after melting, thermal poling is considered a promising candidate for post-melt processing of glasses. However, in order to take full advantage of this… read more here.
Keywords: thermal poling; molecular dynamics; glass; using molecular ... See more keywords
Modeling the thermal poling of glasses using molecular dynamics. Part 2: Effects on elastic properties
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Non-crystalline Solids"
DOI: 10.1016/j.jnoncrysol.2017.04.017
Abstract: Abstract In this work, thermal poling of ternary oxide glasses, including borosilicates and aluminosilicates, is studied using molecular dynamics. For the glass compositions simulated, results show that thermal poling lowers the Young's modulus of those… read more here.
Keywords: thermal poling; molecular dynamics; using molecular; oxide glasses ... See more keywords
Identification of potential SARS-CoV-2 inhibitors from South African medicinal plant extracts using molecular modelling approaches
Sign Up to like & getrecommendations! Published in 2020 at "South African Journal of Botany"
DOI: 10.1016/j.sajb.2020.07.035
Abstract: Abstract The coronavirus is a group of viruses found in animals as well as humans and have been detected since the 1960s. However, a newly identified form, SARS-CoV-2, has triggered a recent pandemic of respiratory… read more here.
Keywords: using molecular; south african; bioactive compounds; african medicinal ... See more keywords
In vivo and in vitro α-amanitin metabolism studies using molecular networking.
Sign Up to like & getrecommendations! Published in 2021 at "Toxicology letters"
DOI: 10.1016/j.toxlet.2021.04.006
Abstract: Amanitin poisonings are among the most life-threatening mushroom poisonings, and are mainly caused by the genus Amanita. Hepatotoxicity is the hallmark of amanitins, powerful toxins contained in these mushrooms, and can require liver transplant. Among… read more here.
Keywords: metabolism; molecular networking; amanitin metabolism; using molecular ... See more keywords
Evaluating the Ability of Selected Force Fields to Simulate Hydrocarbons as a Function of Temperature and Pressure Using Molecular Dynamics
Sign Up to like & getrecommendations! Published in 2021 at "Energy & Fuels"
DOI: 10.1021/acs.energyfuels.0c03363
Abstract: The ability of both nonreactive (OPLS-AA) and reactive (AIREBO-M and ReaxFF) force fields to model pure hydrocarbon fluids at various temperatures and pressures was assessed using molecular dynamic... read more here.
Keywords: force fields; using molecular; ability selected; evaluating ability ... See more keywords
Fighting COVID-19 Using Molecular Dynamics Simulations
Sign Up to like & getrecommendations! Published in 2020 at "ACS Central Science"
DOI: 10.1021/acscentsci.0c01236
Abstract: Molecular dynamics simulations revealed a promising immune target on the SARS-CoV-2 spike protein, proposing novel strategies for vaccine development. read more here.
Keywords: covid using; molecular dynamics; using molecular; fighting covid ... See more keywords