Theoretical methods for the simulation of nucleic acids.
Different 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.
Orozco
Modesto
M
Institut de Recerca Biomèdica, Parc Científic de Barcelona, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Barcelona E-08028, Spain.
Pérez
Alberto
A
Noy
Agnes
A
Luque
F Javier
FJ
D001483:Base Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D013816:Thermodynamics
D009696:Nucleic Acids