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Alexander Heifetz - Quantum Mechanics in Drug Discovery

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Alexander Heifetz Quantum Mechanics in Drug Discovery
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Volume 2114 Methods in Molecular Biology Series Editor John M Walker School - photo 1
Volume 2114
Methods in Molecular Biology
Series Editor
John M. Walker
School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, UK

For further volumes: http://www.springer.com/series/7651

For over 35 years, biological scientists have come to rely on the research protocols and methodologies in the critically acclaimedMethods in Molecular Biologyseries. The series was the first to introduce the step-by-step protocols approach that has become the standard in all biomedical protocol publishing. Each protocol is provided in readily-reproducible step-by-step fashion, opening with an introductory overview, a list of the materials and reagents needed to complete the experiment, and followed by a detailed procedure that is supported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitute the key ingredient in each and every volume of theMethods in Molecular Biologyseries. Tested and trusted, comprehensive and reliable, all protocols from the series are indexed in PubMed.

Editor
Alexander Heifetz
Quantum Mechanics in Drug Discovery
Editor Alexander Heifetz Evotec UK Ltd Abingdon Oxfordshire UK ISSN - photo 2
Editor
Alexander Heifetz
Evotec (UK) Ltd., Abingdon, Oxfordshire, UK
ISSN 1064-3745 e-ISSN 1940-6029
Methods in Molecular Biology
ISBN 978-1-0716-0281-2 e-ISBN 978-1-0716-0282-9
https://doi.org/10.1007/978-1-0716-0282-9
Springer Science+Business Media, LLC, part of Springer Nature 2020
This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed.
The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use.
The publisher, the authors, and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This Humana imprint is published by the registered company Springer Science+Business Media, LLC, part of Springer Nature.

The registered company address is: 1 New York Plaza, New York, NY 10004, U.S.A.

Preface

The application of quantum mechanical (QM) methods in drug discovery is becoming increasingly popular. This is largely a consequence of significant improvements in computing power/speed, which have led to advances in QM algorithm development and new applications of QM methods. Such methods are now routinely applied to many computer-aided drug discovery problems, including characterizing proteinwaterligand and proteinprotein interactions, providing estimates of binding affinities, determining ligand energies and bioactive conformations, refinement of molecular geometries, scoring docked proteinligand poses, describing molecular similarity, structureactivity relationship (SAR) analysis, and ADMET prediction. QM applications are rapidly replacing classical molecular mechanics (MM) methods because there is no need to use MM approximations when you can perform QM calculations with much higher accuracy and similar speed.

This book provides a unique overview of the QM methods, protocols, and applications used to deal with various challenges in drug discovery and structure exploration. It compares the performance of QM methods with alternative computational approaches such as molecular mechanics. Finally, the book provides an overall perspective on QM methods and their role in drug discovery. A review of these techniques will allow a diverse audience, including structural and molecular biologists, computational and medicinal chemists, pharmacologists and drug designers, to navigate through and effectively deploy these advances.
The most intelligent picture ever taken Participants of the 5th Solvay - photo 3

The most intelligent picture ever taken

Participants of the 5th Solvay Conference on Quantum Mechanics, 1927; 17 of the 29 attendees were or became Nobel Prize winners, including Marie Curie, who, alone among them, had won Nobel Prizes in two separate scientific disciplines.

From back to front and from left to right: Auguste Piccard, mile Henriot, Paul Ehrenfest, douard Herzen, Thophile de Donder, Erwin Schrdinger, Jules-mile Verschaffelt, Wolfgang Pauli, Werner Heisenberg, Ralph Howard Fowler, Lon Brillouin, Peter Debye, Martin Knudsen, William Lawrence Bragg, Hendrik Anthony Kramers, Paul Dirac, Arthur Compton, Louis de Broglie, Max Born, Niels Bohr, Irving Langmuir, Max Planck, Marie Skodowska Curie, Hendrik Lorentz, Albert Einstein, Paul Langevin, Charles Eugne Guye, Charles Thomson Rees Wilson, Owen Willans Richardson.

Alexander Heifetz
Oxfordshire, UK
Contents
Christofer S. Tautermann
Jinfeng Liu and Xiao He
Alexander Heifetz , Tim James , Michelle Southey , Mike J. Bodkin and Steven Bromidge
Dmitri G. Fedorov
Andrew Anighoro
Hiroya Nakata and Dmitri G. Fedorov
Yoshio Okiyama , Kaori Fukuzawa , Yuto Komeiji and Shigenori Tanaka
Dmitri G. Fedorov , Hui Li , Vladimir Mironov and Yuri Alexeev
Inaki Morao , Alexander Heifetz and Dmitri G. Fedorov
Stephan Irle , Van Q. Vuong , Mouhmad H. Elayyan , Marat R. Talipov and Steven M. Abel
Alexander Heifetz , Tim James , Michelle Southey , Inaki Morao , Dmitri G. Fedorov , Mike J. Bodkin and Andrea Townsend-Nicholson
Alexander Heifetz and Andrea Townsend-Nicholson
Alexander Heifetz , Vladimir Sladek , Andrea Townsend-Nicholson and Dmitri G. Fedorov
Matthew Habgood , Tim James and Alexander Heifetz
Martin Kotev , Laurie Sarrat and Constantino Diaz Gonzalez
Claudio N. Cavasotto
M. Gabriela Aucar and Claudio N. Cavasotto
Alfonso Pozzan
Alessio Lodola , Donatella Callegari , Laura Scalvini , Silvia Rivara and Marco Mor
Richard A. Bryce
Contributors
Steven M. Abel
Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA
Yuri Alexeev
Argonne Leadership Computing Facility and Computational Science Division, Argonne National Laboratory, Lemont, IL, USA
Andrew Anighoro
Evotec (UK) Ltd., Oxfordshire, UK
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