Unravelling viral dynamics through molecular dynamics simulations - A brief overview

Viruses are a class of complex and dynamic macromolecular machines that can virtually infect all known life forms in the biosphere. This remarkable complexity results from a unique organization involving protein (capsid) and nucleic acid (DNA/RNA). A virus structure is metastable and highly responsive to environmental changes. Although major events of a virus life cycle are well characterized, several important questions with respect to how the nucleocapsid assemble/disassemble remain to be explored. In recent years due to enhanced computational power, molecular dynamics (MD) simulations have become an attractive alternative for addressing these questions since it is challenging to probe dynamic behavior with in vitro experimentation. The ability to simulate a complete virus particle provides an unprecedented atomic level resolution which can be used to understand its behavior under specific conditions. The current review outlines contributions made by all-atom and coarse-grained MD simulations towards understanding the mechanics and dynamics of virus structure and function. Databases and programs which facilitate such in silico investigations have also been discussed.