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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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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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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