Dependence of A-RNA simulations on the choice of the force field and salt strength

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F09%3A00037460" target="_blank" >RIV/00216224:14310/09:00037460 - isvavai.cz</a>

Alternative codes found

RIV/68081707:_____/09:00333332 RIV/61989592:15310/09:00010143

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Dependence of A-RNA simulations on the choice of the force field and salt strength

Original language description

We carried out an extensive molecular dynamics study on three A-RNA duplexes. Dependence of the A-RNA geometry on force fields (Parm99 and Parmbsc0) and salt strength conditions was investigated. The Parmbsc0 force field makes the A-RNA duplex more compact in comparison to the Parm99 by preventing temporary alfa/gama t/t flips common in Parm99 simulations. The stabilization of the A-RNA helices caused by the Parmbsc0 force field includes visible reduction of the major groove width, increase of the basepair roll, larger helical inclination and small increases of twist. Therefore, the Parmbsc0 shifts the simulated duplexes more deeply into the A-form.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

BO - Biophysics

OECD FORD branch

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Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>Z - Vyzkumny zamer (s odkazem do CEZ)

Publication year

2009

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Physical Chemistry Chemical Physics

ISSN

1463-9076

e-ISSN

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Volume of the periodical

11

Issue of the periodical within the volume

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Country of publishing house

CZ - CZECH REPUBLIC

Number of pages

11

Pages from-to

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UT code for WoS article

000271907200016

EID of the result in the Scopus database

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