Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields.

ABSTRACT: Recent modifications and improvements to standard nucleic acid force fields have attempted to fix problems and issues that have been observed as longer timescale simulations have become routine. Although previous work has shown the ability to fold the UUCG stem-loop structure, until now no group has attempted to quantify the performance of current force fields using highly converged structural populations of the tetraloop conformational ensemble. In this study, we report the use of multiple independent sets of multidimensional replica exchange molecular dynamics (M-REMD) simulations with different initial conditions to generate well-converged conformational ensembles for the tetranucleotides r(GACC) and r(CCCC), as well as the larger UUCG tetraloop motif. By generating what is to our knowl

SUBMITTER: Bergonzo C 

PROVIDER: S-EPMC4536319 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature