Table of Contents

Part I: Chemical Space 1. Investigation of the Click-Chemical Space for Drug Design Using ZINClick

Alberto Massarotti

2. Molecular Scaffold Hopping via Holistic Molecular Representation

Francesca Grisoni and Gisbert Schneider

Part II: Hit Identification and Hit-to-Lead Optimization 3. Biased Docking for Protein-Ligand Pose Prediction

Juan Pablo Arcon, Adrian G. Turjanski, Marcelo A. Marti, and Stefano Forli

4. Binding Mode Prediction and Virtual Screening Applications by Covalent Docking

Andrea Scarpino, Gyoergy G. Ferenczy, and Gyoergy M. Keseru

5. Ligand-Receptor, Ligand-DNA Interactions and Drug Design

Aggeliki Syriopoulou, Ioannis Markopoulos, Andreas G. Tzakos, and Thomas Mavromoustakos

6. Simulation of Ligand Transport in Receptors Using CaverDock

Jana Hozzova, Ondrej Vavra, David Bednar, and Jiri Filipovic

7. Negative Image-Based Screening: Rigid Docking Using Cavity Information

Pekka A. Postila, Sami T. Kurkinen, and Olli T. Pentikainen

8. Negative Image-Based Rescoring: Using Cavity Information to Improve Docking Screening

Olli T. Pentikainen and Pekka A. Postila

9. Fragment-Based Drug Design of Selective HDAC6 Inhibitors

Dusan Ruzic, Nemanja Djokovic, and Katarina Nikolic

10. A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time

Gaurav K. Ganotra, Ariane Nunes-Alves, and Rebecca C. Wade

11. Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level

Gert-Jan Bekker and Narutoshi Kamiya

12. Free Energy Calculations for Protein-Ligand Binding Prediction

Willem Jespers, Johan Aqvist, and Hugo Gutierrez-de-Teran

13. Exploiting Water Dynamics for Pharmacophore Screening

David Schaller, Szymon Pach, Marcel Bermudez, and Gerhard Wolber

14. Markov State Models to Elucidate Ligand Binding Mechanism

Yunhui Ge and Vincent A. Voelz

Part III: Target Identification 15. From Homology Modeling to the Hit Identification and Drug Repurposing: A Structure-Based Approach in the Discovery of Novel Potential Anti-Obesity Compounds

Giosue Costa, Anna Artese, Francesco Ortuso, and Stefano Alcaro

16. Multiple Target Drug Design Using LigBuilder 3

Xiaoyu Qing, Shiwei Wang, Yaxia Yuan, Jianfeng Pei, and Luhua Lai

17. Bionoi: A Voronoi Diagram-Based Representation of Ligand-Binding Sites in Proteins for Machine Learning Applications

Joseph Feinstein, Wentao Shi, J. Ramanujam, and Michal Brylinski

18. MDock: A Suite for Molecular Inverse Docking and Target Prediction

Zhiwei Ma and Xiaoqin Zou

About the Author

Flavio Ballante is a researcher in the Department of Cell and Molecular Biology at Uppsala University (Sweden). He graduated in Medicinal Chemistry from Sapienza University in Rome (Italy) where he also obtained a Ph.D. in Pharmaceutical Sciences. During his academic career, he conducted research in France (University of Lorraine, Metz), the USA (Washington University School of Medicine in St. Louis, MO), and Sweden (Uppsala University, Uppsala), working on computer-aided drug design, chemistry, and biology experiments. His primary research goals are directed toward understanding the basis for molecular recognition at the atomic level, and his scientific activity is mainly focused on the design, development, and application of computational methods for ligand discovery.