Multiscale Approaches to Protein Modeling Structure Prediction, Dyna
Multiscale Approaches to Protein Modeling is a comprehensive review of the most advanced multiscale methods for protein structure prediction, computational studies of protein dynamics, folding mechanisms and macromolecular interactions. The approaches spa
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Andrzej Kolinski Editor
Multiscale Approaches to Protein Modeling
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Editor Andrzej Kolinski Department of Chemistry University of Warsaw ul. Pasteura 1 02-093 Warszawa Poland [email protected]
ISBN 978-1-4419-6888-3 e-ISBN 978-1-4419-6889-0 DOI 10.1007/978-1-4419-6889-0 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2010934732 © Springer Science+Business Media, LLC 2011 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com)
Preface
Thanks to enormous progress in sequencing of genomic data, presently we know millions of protein sequences. At the same time the number of experimentally solved protein structures is much smaller, ca. 60,000. This is because of large cost of structure determination. Thus, the theoretical in silico prediction of protein structures and dynamics is essential for understanding the molecular basis of drug action, metabolic and signaling pathways in living cells, and designing new technologies in the life science and material sciences. Unfortunately, a “brute force” approach remains impractical. Folding of a typical protein (in vivo or in vitro) takes milliseconds to minutes, while the state-of-the-art all-atom molecular mechanics simulations of protein systems can cover only a time period of nanoseconds to microseconds. This is the reason for the enormous progress in the development of various multiscale modeling techniques applied to protein structure prediction, modeling of protein dynamics and folding pathways, in silico protein engineering, model-aided interpretation of experimental data, modeling of macromolecular assemblies, and theoretical studies of protein thermodynamics. Coarse-graining of the proteins’ conformational space is a common feature of all these approaches, although the details and the underlying physical models span a very broad spectrum. This book contains comprehensive reviews of the most advanced multiscale modeling methods in protein structure prediction, computational studies of protein dynamics, folding mechanisms, and macromolecular interactions. The presented approaches span a wide range of the levels of coarse-grained representations, various sampling techniques, and a variety of applications to biomedical and biophysical problems. It was our intention t
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