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Molecular dynamics simulations: advances and applications.

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.

SUBMITTER: Hospital A 

PROVIDER: S-EPMC4655909 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Molecular dynamics simulations: advances and applications.

Hospital Adam A   Goñi Josep Ramon JR   Orozco Modesto M   Gelpí Josep L JL  

Advances and applications in bioinformatics and chemistry : AABC 20151119

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 th  ...[more]

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