Quantum mechanics in drug discovery
Author(s)
Bibliographic Information
Quantum mechanics in drug discovery
（Methods in molecular biology / John M. Walker, series editor, 2114）（Springer protocols）
Humana Press, c2020
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Note
Includes bibliographical references and index
Description and Table of Contents
Description
This volume looks at applications of quantum mechanical (QM) methods in drug discovery. The chapters in this book describe how QM approaches can be applied to address key drug discovery issues, such as characterizing protein-water-ligand and protein-protein interactions, providing estimates of binding affinities, determining ligand energies and bioactive conformations, refinement of molecular geometries, scoring docked protein-ligand poses, describing molecular similarity, structure-activity-relationship (SAR) analysis, and ADMET prediction. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary software and tools, step-by-step, readily reproducible modeling protocols, and tips on troubleshooting and avoiding known pitfalls.
Cutting-edge and unique, Quantum Mechanics in Drug Discovery is a valuable resource for structural and molecular biologists, computational and medicinal chemists, pharmacologists, and drug designers.
Table of Contents
1. Current and Future Challenges in Modern Drug Discovery
Christofer S. Tautermann
2. QM Implementation in Drug Design: Does It Really Help?
Jinfeng Liu and Xiao He
3. Guiding Medicinal Chemistry with Fragment Molecular Orbital (FMO) Method
Alexander Heifetz, Tim James, Michelle Southey, Mike Bodkin, and Steven Bromidge
4. Analyzing Interactions with the Fragment Molecular Orbital Method
Dmitri G. Fedorov
5. Underappreciated Chemical Interactions in Protein-Ligand Complexes
Andrew Anighoro
6. Geometry Optimization, Transition State Search, and Reaction Path Mapping Accomplished with the Fragment Molecular Orbital Method
Hiroya Nakata and Dmitri G. Fedorov
7. Taking Water into Account with the Fragment Molecular Orbital Method
Yoshio Okiyama, Kaori Fukuzawa, Yuto Komeiji, and Shigenori Tanaka
8. Computational Methods for Biochemical Simulations Implemented in GAMESS
Dmitri G. Fedorov, Hui Li, Vladimir Mironov, and Yuri Alexeev
9. QM in Seconds with the Fragment Molecular Orbital and Density-Functional Tight-Binding Methods
Inaki Morao, Alexander Heifetz, and Dmitri G. Fedorov
10. Protein Molecular Dynamics Simulations with Approximate QM: What Can We Learn?
Stephan Irle, Van Q. Vuong, Mouhmad H. Elayyan, Marat R. Talipov, and Steven M. Abel
11. Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method
Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Dmitri G. Fedorov, Mike J. Bodkin, and Andrea Townsend-Nicholson
12. Characterizing Rhodopsin-Arrestin Interactions with the Fragment Molecular Orbital (FMO) Method
Alexander Heifetz and Andrea Townsend-Nicholson
13. Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method
Alexander Heifetz, Vladimir Sladek, Andrea Townsend-Nicholson, and Dmitri G. Fedorov
14. Conformational Searching with Quantum Mechanics
Matthew Habgood, Tim James, and Alexander Heifetz
15. User-Friendly Quantum Mechanics: Applications for Drug Discovery
Martin Kotev, Laurie Sarrat, and Constantino Diaz Gonzalez
16. Binding Free Energy Calculation Using Quantum Mechanics Aimed for Drug Lead Optimization
Claudio N. Cavasotto
17. Molecular Docking Using Quantum Mechanical-Based Methods
M. Gabriela Aucar and Claudio N. Cavasotto
18. QM Calculations in ADMET Prediction
Alfonso Pozzan
19. Design and SAR Analysis of Covalent Inhibitors Driven by Hybrid QM/MM Simulations
Alessio Lodola, Donatella Callegari, Laura Scalvini, Silvia Rivara, and Marco Mor
20. What's Next for Quantum Mechanics in Structure-Based Drug Discovery?
Richard A. Bryce
by "Nielsen BookData"