Computational Virology: Molecular Simulations of Virus Dynamics and Interactions

Molecular modelling and simulations play a key role in computational virology, allowing us to study viruses and their components. This allows experimental structures and related information to be integrated into a single coherent model, enabling predictions about the behaviour of a viral system to go beyond what could be obtained experimentally. In this way, computational approaches provide a powerful complement to more traditional experimental and structural methods. In this chapter, we describe three main areas of computational virology to showcase the power of methods within this field. We begin by describing relatively small simulation systems and focusing on the behaviour of fusion peptides. Then, extending to longer timescales and larger systems, we discuss computational studies of viral capsid assembly and genome encapsidation. Finally, we describe recent developments which allow entire viral particles to be simulated.