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A Practical Introduction to Molecular Dynamics Simulations: Applications to Homology Modeling

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Book cover Homology Modeling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 857))

Abstract

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.

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Acknowledgments

This work was supported in part by grant 09-LR-06-117792-WALR from the University of California Lab Fees program (RCW) and grant NSF1047875 from the US National Science Foundation (RCW). We additionally thank the NSF TeraGrid (award TG-MCB090110) for providing supercomputer time in support of this work. We would also like to thank Weihua Li and Yun Tang of the School of Pharmacy, East China University of Science and Technology for their fast response and willingness to share with us their P450 2J2 homology structure. We thank Pr. Pierre-Alain Carrupt (School of Pharmaceutical Sciences, University of Geneva, University of Lausanne) for technical support.

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Authors and Affiliations

  1. School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland

    Alessandra Nurisso & Antoine Daina

  2. Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA

    Ross C. Walker

  3. San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA

    Ross C. Walker

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  1. Alessandra Nurisso
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  2. Antoine Daina
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  3. Ross C. Walker
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Correspondence to Ross C. Walker .

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  1. Molsoft L.L.C., Sorrento Valley Road 11199, S209 San Diego, 92121, California, USA

    Andrew J. W. Orry

  2. Skaggs School of Pharmacy &, Pharmaceutical Sciences, University of California, San Diego, Gilman Drive 9500, La Jolla, 92093, California, USA

    Ruben Abagyan

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Nurisso, A., Daina, A., Walker, R.C. (2011). A Practical Introduction to Molecular Dynamics Simulations: Applications to Homology Modeling. In: Orry, A., Abagyan, R. (eds) Homology Modeling. Methods in Molecular Biology, vol 857. Humana Press. https://doi.org/10.1007/978-1-61779-588-6_6

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  • DOI: https://doi.org/10.1007/978-1-61779-588-6_6

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