Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.
J Phys Chem Lett
; 5(10): 1771-82, 2014 May 15.
Article
em En
| MEDLINE
| ID: mdl-26270382
ABSTRACT
We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.
Texto completo:
1
Base de dados:
MEDLINE
Idioma:
En
Ano de publicação:
2014
Tipo de documento:
Article