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- W2614722686 abstract "Our interest has been focused on molecular modelling studies ofDNA quadruplexes. Since these four-stranded arrangements playimportant role in cell cycle, they are currently extensivelystudied by means of experimental and computational techniques.Human telomeric sequence was extensively studied by means ofmolecular modelling tools. Starting from the X-ray structure wetested the influence of various ion types and radii onmolecular dynamics, Locally Enhanced Sampling, free energyestimations, etc. Results have shown a strong influence of ionradius on conformational behavior during the trajectories.Greater computational force brings not only larger simulationtimescale, but also cumulation of force-field imbalancies whichcan lead to some artifacts. Simple model of ion descriptioninfluences entire potential energy surface and may shift themolecule from experimetal geometry. Slight changes in ionparameters force the simulation to completely different area ofconformational space. Some (ir)reversible backbone changes ofalpha-beta-gamma torsion angles (switches) have been observedin all trajectories that pointed out at some imbalancies in theforce field parametrisation. Our study brought a contributionto some methodological tasks such as inclusions of proper ionstype or backbone torsions switches. It has shown that humantelomere sequence can be used as a testing example for recentmethodological problems, because some imbalancies appear in itin relativelly short simulation time." @default.
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- W2614722686 date "2007-01-01" @default.
- W2614722686 modified "2023-10-16" @default.
- W2614722686 title "Human telomeric G-DNA - a test example for force fieldadjustment" @default.
- W2614722686 hasPublicationYear "2007" @default.
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