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Understanding RNA flexibility using explicit solvent simulations: The ribosomal and group I intron reverse kink-turn motifs

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    0370399 - BFÚ 2012 RIV US eng J - Journal Article
    Sklenovský, P. - Florová, P. - Banáš, P. - Réblová, Kamila - Lankaš, Filip - Otyepka, M. - Šponer, Jiří
    Understanding RNA flexibility using explicit solvent simulations: The ribosomal and group I intron reverse kink-turn motifs.
    Journal of Chemical Theory and Computation. Roč. 7, č. 9 (2011), s. 2963-2980. ISSN 1549-9618. E-ISSN 1549-9626
    R&D Projects: GA ČR(CZ) GD203/09/H046; GA AV ČR(CZ) IAA400040802; GA MŠMT(CZ) LC512; GA AV ČR(CZ) KJB400040901; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822; GA MŠMT(CZ) LC06030
    Grant - others:GA ČR(CZ) GPP301/11/P558
    Program: GP
    Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z40550506
    Keywords : reverse kink-turn * simulation * flexibility
    Subject RIV: BO - Biophysics
    Impact factor: 5.215, year: 2011

    We report unrestrained, explicit solvent molecular dynamics simulations of ribosomal and intron reverse kink-turns (54 simulations in total) with different variants (ff94, ff99, ff99bsc0, ff99chiOL, and ff99bsc0chiOL) of the Cornell et al. force field. The simulations characterize the directional intrinsic flexibility of reverse kink-turns pertinent to their folded functional geometries.
    Permanent Link: http://hdl.handle.net/11104/0204220

     
     
Number of the records: 1  

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