Molecular-Level Simulation of Pandemic Influenza Glycoproteins

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 819)

Abstract

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 

Notes

Acknowledgments

This work was funded by the National Institutes of Health (NIH) through the NIH Director’s New Innovator Award Program, 1-DP2-OD007237 and a NIH Career Transition Award 1-K22-AI081901 to R.E.A. W.W.L. is funded in part by NIH P41 RR08605.

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Departments of Pharmaceutical Sciences, Computer Science, and ChemistryUniversity of CaliforniaIrvineUSA
  2. 2.National Biomedical Computation ResourceUniversity of California, San DiegoLa JollaUSA

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