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. 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 Hozzová, Ondrej Vávra, David Bednár, and Jirí Filipovic 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 16. Multiple Target Drug Design Using LigBuilder 3 Xiaoyu Qing, Shiwei Wang, Yaxia Yuan, Jianfeng Pe