Computational Systems Pharmacology and Toxicology
CHAPTER 7: In silico Chemical–Protein Docking and Molecular Dynamics
Published:01 Mar 2017
Special Collection: 2017 ebook collectionSeries: Issues in Toxicology
Sanjeeva J. Wijeyesakere, Rudy J. Richardson, 2017. "In silico Chemical–Protein Docking and Molecular Dynamics", Computational Systems Pharmacology and Toxicology, Rudy J Richardson, Dale E Johnson
Download citation file:
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.