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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 resourcefor structural and molecular biologists, computational and medicinal chemists, pharmacologists, and drug designers.
List of contents
Current and Future Challenges in Modern Drug Discovery.- QM Implementation in Drug Design: Does It Really Help?.- Guiding Medicinal Chemistry with Fragment Molecular Orbital (FMO) Method.- Analyzing Interactions with the Fragment Molecular Orbital Method.- Underappreciated Chemical Interactions in Protein-Ligand Complexes.- Geometry Optimization, Transition State Search, and Reaction Path Mapping Accomplished with the Fragment Molecular Orbital Method.- Taking Water into Account with the Fragment Molecular Orbital Method.- Computational Methods for Biochemical Simulations Implemented in GAMESS.- QM in Seconds with the Fragment Molecular Orbital and Density-Functional Tight-Binding Methods.- Protein Molecular Dynamics Simulations with Approximate QM: What Can We Learn?.- Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method.- Characterizing Rhodopsin-Arrestin Interactions with the Fragment Molecular Orbital (FMO) Method.- Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method.- Conformational Searching with Quantum Mechanics.- User-Friendly Quantum Mechanics: Applications for Drug Discovery.- Binding Free Energy Calculation Using Quantum Mechanics Aimed for Drug Lead Optimization.- Molecular Docking Using Quantum Mechanical-Based Methods.- QM Calculations in ADMET Prediction.- Design and SAR Analysis of Covalent Inhibitors Driven by Hybrid QM/MM Simulations.- What's Next for Quantum Mechanics in Structure-Based Drug Discovery?.
