Number of the records: 1

Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins

SYSNO ASEP	0353763
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins
Author(s)	Banáš, P. (CZ) Hollas, D. (CZ) Zgarbová, M. (CZ) Jurečka, P. (CZ) Orozco, M. (ES) Cheatham III, T.E. (US) Šponer, Jiří (BFU-R)_{RID, ORCID} Otyepka, M. (CZ)
Number of authors	8
Source Title	Journal of Chemical Theory and Computation . - : American Chemical Society - ISSN 1549-9618 Roč. 6, č. 12 (2010), s. 3836-3849
Number of pages	14 s.
Language	eng - English
Country	US - United States
Keywords	molecular dynamics ; force fields ; RNA ; tetraloops
Subject RIV	BO - Biophysics
R&D Projects	LC06030 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
	GA203/09/1476 GA ČR - Czech Science Foundation (CSF)
	GD203/09/H046 GA ČR - Czech Science Foundation (CSF)
	IAA400040802 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR)
CEZ	AV0Z50040507 - BFU-R (2005-2011)
	AV0Z50040702 - BFU-R (2007-2013)
UT WOS	000285217000019
DOI	10.1021/ct100481h
Annotation	The RNA hairpin loops represent important RNA topologies with indispensable biological functions in RNA folding and tertiary interactions. Explicit solvent molecular dynamics (MD) simulation is a computational technique which can efficiently complement the experimental data and provide unique structural dynamics information on the atomic scale. Nevertheless, outcome of simulations is often compromised by imperfections in parameterization of simplified pair-wise additive empirical potentials referred also as force fields. We have pointed out in several recent studies that force field description of single stranded hairpin segments of nucleic acids may be particularly challenging for the force fields. In this paper, we report a critical assessment of a broad set of MD simulations of UUCG, GAGA, and GAAA tetraloops using various force fields.
Workplace	Institute of Biophysics
Contact	Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244
Year of Publishing	2011

Number of the records: 1