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Protein-Ligand Interactions and Drug Design
Paperback
Series: Methods in Molecular Biology, Book 2266
ISBN13: 9781071612118
Publisher: Humana Pr
Published: Mar 24 2022
Pages: 327
Weight: 1.32
Height: 0.72 Width: 7.00 Depth: 10.00
Language: English
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
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, 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
16. Multiple Target Drug Design Using LigBuilder 3
Xiaoyu Qing, Shiwei Wang, Yaxia Yuan, Jianfeng Pe
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