Computational Methods in Protein Evolution
This volume presents a diverse collection of methodologies used to study various problems at the protein sequence and structure level. The chapters in this book look at issues ranging from broad concepts like protein space to specifics like antibody model
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Tobias Sikosek Editor
Computational Methods in Protein Evolution
METHODS
IN
MOLECULAR BIOLOGY
Series Editor John M. Walker School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB, UK
For further volumes: http://www.springer.com/series/7651
Computational Methods in Protein Evolution Edited by
Tobias Sikosek GlaxoSmithKline, Cellzome - a GSK company, Meyerhofstrasse 1, Heidelberg, Baden-Württemberg, Germany
Editor Tobias Sikosek GlaxoSmithKline Cellzome - a GSK company Meyerhofstrasse 1 Heidelberg, Baden-Wu¨rttemberg, Germany
ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-8735-1 ISBN 978-1-4939-8736-8 (eBook) https://doi.org/10.1007/978-1-4939-8736-8 Library of Congress Control Number: 2018954227 © Springer Science+Business Media, LLC, part of Springer Nature 2019, corrected publication 2019 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, express 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 Press imprint is published by the registered company Springer Science+Business Media, LLC, part of Springer Nature. The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A.
Preface Proteins are the most versatile kind of molecule that we know and the result of a long evolutionary process. During this process, countless rearranging, mutating, and replicating strands of DNA have managed to both encode and conserve proteins that would allow them to replicate and stay intact and on the other hand have allowed their proteins to change and ultimately help them replicate more than other strands of DNA. All cells make proteins in their protein factories called ribosomes, where the DNA of a gene is translated according to the ancient genetic code into strings of amino acids which follow the laws of thermodynamics and molecular forces to fold up into specific wobbly three-dimensional shapes. Protein evol
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