In this chapter, practical concepts and guidelines are provided for the use of molecular dynamics (MD) simulation for the refinement of homology models. First, an overview of the history and a theoretical background of MD are given. Literature examples of successful MD refinement of homology models are reviewed before selecting the Cytochrome P450 2J2 structure as a case study. We describe the setup of a system for classical MD simulation in a detailed stepwise fashion and how to perform the refinement described in the publication of Li et al. (Proteins 71:938-949, 2008). This tutorial is based on version 11 of the AMBER Molecular Dynamics software package ( http://ambermd.org/ ). However, the approach discussed is equally applicable to any condensed phase MD simulation environment. © 2011 Springer Science+Business Media,LLC.
CITATION STYLE
Nurisso, A., Daina, A., & Walker, R. C. (2012). A practical introduction to molecular dynamics simulations: Applications to homology modeling. Methods in Molecular Biology, 857, 137–173. https://doi.org/10.1007/978-1-61779-588-6_6
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