**Author details**

*Molecular Docking and Molecular Dynamics*

*polarity (pink: nonpolar; green: polar uncharged).*

**5. Conclusions**

**Figure 11.**

**Acknowledgements**

**Conflict of interest**

a Fulbright Fellowship awarded to S Paula.

The authors declare no conflicts of interest.

Using the AhR and substituted phenylacrylonitriles as an example, we demonstrated the usefulness of a number of computational tools for the study of ligand/ receptor interactions. Homology modeling gave access to the structure of a protein domain that has not yet been solved by X-ray crystallography. The most probable binding site was identified, allowing for the docking of ligands, along with a good estimate of their affinities. The identification of this docking site was consistent with subsequent compound design and biological data obtained [10]. MD simulations validated the stability of docked poses and illustrated the role of solvent molecules in the binding pocket. The value of the described techniques lies in their ability to rapidly evaluate the potential of a new ligand in silico before spending precious time and resource on its synthesis and experimental evaluation.

*MD simulations. (A) Ligand/AhR complex before (gray) and after (blue) 100 ns of simulation time. (B) Density of water molecules in the binding site as highlighted by orange grids. Residues are colored according to their* 

JR Baker is the grateful recipient of an Australian Government Research Training Program (RTP) scholarship. This work was conducted in part under the auspices of

**14**

Stefan Paula1 \*, Jennifer R. Baker2 , Xiao Zhu3 and Adam McCluskey2

1 Department of Chemistry, Purdue University, West Lafayette, Indiana, USA

2 Centre for Chemical Biology, Chemistry, School of Environmental Life Science, The University of Newcastle, Callaghan, New South Wales, Australia

3 Research Computing, Information Technology at Purdue (ITaP), Purdue University, West Lafayette, IN, USA

\*Address all correspondence to: paulas@purdue.edu

© 2019 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
