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, Adrián G. Turjanski, Marcelo A. Martí, and Stefano Forli

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

Andrea Scarpino, György G. Ferenczy, and György M. Keserű

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

6. Simulation of Ligand Transport in Receptors Using CaverDock

Jana Hozzová, Ondřej Vávra, David Bednář, and Jiří Filipovič

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

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

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

Olli T. Pentikäinen 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 Åqvist, and Hugo Gutiérrez-de-Terán

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

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

Xiaoyu Qing, Shiwei Wang, Yaxia Yuan, Jianfeng Pe