Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review.
Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a sign...
| Publicado en: | BioMed Research International Vol. 2015; pp. 1 - 19 |
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| Autores principales: | , |
| Formato: | equations & formulas pictorial review Journal Article |
| Publicado: |
Wiley-Blackwell
2/16/2015
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=109273388&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 109273388 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 23146133 FT2T jtl: BioMed Research International issn: 23146133 maglogo: N pubinfo: dt: 2/16/2015 vid: 2015 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 109273388 109273388 109273388 10.1155/2015/183918 109273388 ppf: 1 ppct: 18 formats: fmt: @attributes: type: P tig: atl: Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review. aug: au: Paquet, Eric Viktor, Herna L. affil: Vaccine Program, National Research Council, 1200 Montreal Road, Ottawa, ON, Canada, K1A 0R6 sug: subj: Computer Simulation ab: Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. pubtype: Academic Journal doctype: equations & formulas pictorial review Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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