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Molecular Dynamics and Related Computational Methods with Applications to Drug Discovery

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Coupled Mathematical Models for Physical and Biological Nanoscale Systems and Their Applications (BIRS-16w5069 2016)

Part of the book series: Springer Proceedings in Mathematics & Statistics ((PROMS,volume 232))

Abstract

The main objective of this review chapter is to give the reader a practical toolbox for applications in quantitative biology and computational drug discovery. The computational technique of molecular dynamics is discussed, with special attention to force fields for protein simulations and methods for the calculation of solvation free energies. Additionally, computational methods aimed at characterizing and identifying ligand binding pockets on protein surfaces are discussed. Practical information about available databases and software of use in drug design and discovery is provided.

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Acknowledgements

The authors are grateful to the Natural Sciences and Engineering Research Council of Canada, the Li Ka Shing Institute of Applied Virology and the Alberta Cancer Foundation for funding support.

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Authors and Affiliations

  1. Department of Oncology, University of Alberta, Edmonton, AB, T6G 1Z2, Canada

    Jordane Preto, Philip Winter, Sara Ibrahim Omar & Jack A. Tuszynski

  2. Department of Physics, University of Alberta, Edmonton, AB, T6G 2E1, Canada

    Francesco Gentile, Cassandra Churchill & Jack A. Tuszynski

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  1. Jordane Preto
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  2. Francesco Gentile
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Correspondence to Jack A. Tuszynski .

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Editors and Affiliations

  1. Department of Materials Science and Engineering and G. Millan Institute, Universidad Carlos III de Madrid, Leganés, Spain

    Luis L. Bonilla

  2. Lyman Laboratory of Physics, Department of Physics, Harvard University, Cambridge, Massachusetts, USA

    Efthimios Kaxiras

  3. The MS2 Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada

    Roderick Melnik

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Preto, J., Gentile, F., Winter, P., Churchill, C., Omar, S.I., Tuszynski, J.A. (2018). Molecular Dynamics and Related Computational Methods with Applications to Drug Discovery. In: Bonilla, L., Kaxiras, E., Melnik, R. (eds) Coupled Mathematical Models for Physical and Biological Nanoscale Systems and Their Applications. BIRS-16w5069 2016. Springer Proceedings in Mathematics & Statistics, vol 232. Springer, Cham. https://doi.org/10.1007/978-3-319-76599-0_14

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