Molecular dynamics simulations: advances and applications.

TitleMolecular dynamics simulations: advances and applications.
Publication TypeJournal Article
Year of Publication2015
AuthorsHospital, Adam, Goñi Josep Ramon, Orozco Modesto, and Gelpí Josep-Lluis
JournalAdv Appl Bioinform Chem
Volume8
Pagination37-47
Date Published2015
ISSN1178-6949
Abstract

Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.

DOI10.2147/AABC.S70333
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