CHAPTER 7: In silico Chemical–Protein Docking and Molecular Dynamics
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Published:01 Mar 2017
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Special Collection: 2017 ebook collectionSeries: Issues in Toxicology
S. J. Wijeyesakere and R. J. Richardson, in Computational Systems Pharmacology and Toxicology, ed. R. J. Richardson and D. E. Johnson, The Royal Society of Chemistry, 2017, pp. 174-190.
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This chapter briefly explores the principles and applications to the field of toxicology of two computational structural biology techniques: molecular docking and molecular dynamics (MD) simulations. In general, these in silico approaches enable us to do two important things: (1) gain insight into molecular mechanisms of toxicity; and (2) suggest mechanistic hypotheses for experimental validation or refutation. In addition, through the application of inverse docking and pharmacophore/toxicophore mapping, it is possible to identify potential macromolecular targets of toxicants, including off-targets of pharmaceutical agents. Although docking and MD simulations can be used to examine protein–protein and protein–DNA interactions, our focus is on small-molecule toxicants and protein targets.