Homology Modeling Methods and Protocols
Knowledge about protein tertiary structure can guide experiments, assist in the understanding of structure-function relationships, and aid the design of new therapeutics for disease. Homology modeling is an in silico method that predicts the tertiary stru
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IN
MOLECULAR BIOLOGY™
Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes: http://www.springer.com/series/7651
Homology Modeling Methods and Protocols
Edited by
Andrew J.W. Orry Molsoft L.L.C., San Diego, CA, USA
Ruben Abagyan Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
Editors Andrew J.W. Orry, Ph.D. Molsoft L.L.C. San Diego, CA, USA [email protected]
Ruben Abagyan, Ph.D. Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla, CA, USA and San Diego Supercomputer Center University of California, San Diego La Jolla, CA, USA
ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-61779-587-9 e-ISBN 978-1-61779-588-6 DOI 10.1007/978-1-61779-588-6 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2011945847 © Springer Science+Business Media, LLC 2012 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o 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 Humana Press is part of Springer Science+Business Media (www.springer.com)
Preface Knowledge about protein tertiary structure can guide mutagenesis experiments, help in the understanding of structure–function relationships, and aid the development of new therapeutics for diseases. Homology modeling is an in silico method that predicts the tertiary structure of a query amino acid sequence based on a homologous experimentally determined template structure. The method relies on the observation that the tertiary structure of a protein is better conserved than sequence and therefore two proteins that are not fully conserved at the sequence level may still share the same fold. Structures solved by X-ray crystallography and NMR are deposited in the Protein Data Bank (PDB) and form the templates for homology modeling. The human proteome has approximately 20,000 annotated human proteins and only 4,900 human protein fragments and domains can be found in the PDB. The main steps in a homology modeling experiment are template selection, alignment, backbone and side-chain prediction, and structure optimization, including ligand-guided optimization and evaluation. Errors at the template selection step will result in a
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