Computational Drug Discovery and Design

Volume 819 of the series Methods in Molecular Biology pp 575-594


Molecular-Level Simulation of Pandemic Influenza Glycoproteins

  • Rommie E. AmaroAffiliated withDepartments of Pharmaceutical Sciences, Computer Science, and Chemistry, University of California Email author 
  • , Wilfred W. LiAffiliated withNational Biomedical Computation Resource, University of California, San Diego

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Computational simulation of pandemic diseases provides important insight into many disease features that may benefit public health. This is especially true for the influenza virus, a continuing global pandemic threat. Molecular or atomic-level investigation of influenza has predominantly focused on the two major virus glycoproteins, neuraminidase (NA) and hemagglutinin (HA). In this chapter, we walk the readers through major considerations for studying pandemic influenza glycoproteins, from choosing the most useful choice of system(s) to avoiding common pitfalls in experimental design and execution. While a brief discussion of several potential simulation and docking techniques is presented, we emphasize molecular dynamics (MD) and Brownian dynamics (BD) simulation techniques and molecular docking, within the context of biologically outstanding questions in influenza research.

Key words

Pandemic diseases Computational biology Influenza Neuraminidase Hemagglutinin Molecular dynamics simulations Brownian dynamics simulations Binding free energy estimates Docking Antiviral design