Protein-ligand interactions and drug design
著者
書誌事項
Protein-ligand interactions and drug design
（Methods in molecular biology / John M. Walker, series editor, 2266 ; Springer protocols）（Springer protocols）
Humana Press, c2021
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注記
Includes bibliographical references and index
内容説明・目次
内容説明
This detailed book collects modern and established computer-based methods aimed at addressing the drug discovery challenge from disparate perspectives by exploiting information on ligand-protein recognition. Beginning with methods that allow for the exploration of specific areas of chemical space and the designing of virtual libraries, the volume continues with sections on methods based on docking, quantitative models, and molecular dynamics simulations, which are employed for ligand discovery or development, as well as methods exploiting an ensemble of protein structures for the identification of potential protein targets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Protein-Ligand Interactions and Drug Design provides detailed practical procedures of solid computer-aided drug design methodologies employed to rationalize and optimize protein-ligand interactions, for experienced researchers and novices alike.
目次
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
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