Abstract
Molecular dynamics simulation has developed into a mature technique for effective understanding of structure-function relationships of macromolecules. The present simulation time is close to the chemically relevant time. The collection of information on the dynamic properties of macromolecules is rich enough to change the conventional paradigm of chemical molecular structures from the study of single structures to the analysis of conformational ensembles. Here we describe the fundamentals of molecular dynamics and the improvements in obtaining such an overall direction. The application of this technique to three main problems: allosteric regulation, docking, and structural optimization, is discussed.
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