Parameterization of boronates using VFFDT and Paramfit for molecular dynamics simulation

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dc.authorid0000-0002-1406-0915en_US
dc.authorid0000-0001-9225-7425en_US
dc.contributor.authorKurt, Barış
dc.contributor.authorTemel, Hamdi̊
dc.date.accessioned2021-07-08T11:00:35Z
dc.date.available2021-07-08T11:00:35Z
dc.date.issued2020en_US
dc.departmentDicle Üniversitesi, Fen Bilimleri Enstitüsü, Kimya Ana Bilim Dalıen_US
dc.descriptionWOS:000535695900192
dc.descriptionPMID: 32397128
dc.description.abstractBoric acid, borate esters, and hydroxy derivatives are biologically active molecules. Thus, performing molecular dynamics simulations of these molecules is vital in terms of drug design, but it is difficult to find directly generated Amber parameters based on an ab initio method for these kinds of molecules in the literature. In this study, Amber parameters for such molecules containing boron were generated based on ab initio calculations using the paramfit program, which applies a combination of genetic and simplex algorithms, and the Visual Force Field Derivation Toolkit (VFFDT) program containing the Seminario method. The minimized structure, after obtaining novel parameters and the sander program, was compared with the experimental crystallographic structures, and it was observed that the root-mean-square deviation (RMSD) value between the experimental structure and minimized structure agreed reasonably well. In addition, the molecule was heated, and the molecular dynamics simulation was successfully obtained with the novel parameters.en_US
dc.identifier.citationKurt, B. ve Temel, H. (2020). Parameterization of boronates using VFFDT and Paramfit for molecular dynamics simulation. Molecules, 25(9), 2196.en_US
dc.identifier.doi10.3390/molecules25092196
dc.identifier.issn1420-3049
dc.identifier.issue9en_US
dc.identifier.pmid32397128
dc.identifier.scopus2-s2.0-85084507827
dc.identifier.scopusqualityQ1
dc.identifier.startpage2196en_US
dc.identifier.urihttps://www.mdpi.com/1420-3049/25/9/2196
dc.identifier.urihttps://hdl.handle.net/11468/7220
dc.identifier.volume25en_US
dc.identifier.wosWOS:000535695900192
dc.identifier.wosqualityQ2
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.institutionauthorKurt, Barış
dc.institutionauthorTemel, Hamdi
dc.language.isoenen_US
dc.publisherMDPI AGen_US
dc.relation.ispartofMolecules
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectAmberen_US
dc.subjectBoronen_US
dc.subjectForce fielden_US
dc.subjectParameterizationen_US
dc.titleParameterization of boronates using VFFDT and Paramfit for molecular dynamics simulationen_US
dc.titleParameterization of boronates using VFFDT and Paramfit for molecular dynamics simulation
dc.typeArticleen_US

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