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On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations

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    0334367 - ÚOCHB 2010 RIV GB eng J - Journal Article
    Lankaš, Filip - Gonzalez, O. - Heffler, L. M. - Stoll, G. - Moakher, M. - Maddocks, J. H.
    On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations.
    Physical Chemistry Chemical Physics. Roč. 11, č. 45 (2009), s. 10565-10588. ISSN 1463-9076. E-ISSN 1463-9084
    R&D Projects: GA MŠMT LC512
    Institutional research plan: CEZ:AV0Z40550506
    Keywords : molecular dynamics * coarse-grained models * DNA mechanical properties
    Subject RIV: CF - Physical ; Theoretical Chemistry
    Impact factor: 4.116, year: 2009

    A method is proposed to extract sequence-dependent parameters for rigid base and basepair models of DNA from atomistic molecular dynamics. The practicability of the approach is verified by estimating a complete parameter set for a palindromic oligomer. We test the assumptions of rigidity of the bases and basepairs and the locality of the quadratic internal energy. The results show that these assumptions hold rather well for the base model but not for the basepair model.
    Permanent Link: http://hdl.handle.net/11104/0179121

     
     
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