Theoretical methods for the simulation of nucleic acids

TitleTheoretical methods for the simulation of nucleic acids
Publication TypeJournal Article
Year of Publication2003
AuthorsOrozco, M, Perez A, Noy A, Luque FJ
JournalChemical Society Reviews
Pagination350 - 364
Date Published2003/11//
KeywordsBase Sequence; Computer Simulation; Models, Chemical; Models, Molecular; Nucleic Acid Conformation; Nucleic Acids/chemistry; Thermodynamics
AbstractDifferent theoretical methods for the description of nucleic acid structures are reviewed. Firstly, we introduce the concept of classical force-field in the context of nucleic acid structures, discussing their accuracy. We then examine theoretical approaches to the description of nucleic acids based on: i) a rigid or quasi-rigid description of the molecule, ii) molecular mechanics optimization, and iii) molecular dynamics. Special emphasis is made ion current state of the art molecular dynamics simulations of nucleic acids structures.