Structural Bioinformatics

Informationen zum Autor Jenny Gu, PhD, is Assistant Professor at the Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego. This is her first book. Philip E. Bourne, PhD, is professor in the Department of Pharmacology at the University of California, San Diego, and Director of Integrated Biosciences at the San Diego Supercomputer Center. He is past president of the International Society for Computational Biology (ISCB). He is author of over 125 peer-reviewed scientific papers and four previous books. Klappentext Dieses Lehrbuch vermittelt in der aktualisierten Auflage noch mehr Hintergrundinformationen und praktische Anwendungen der Bioinformatik bei der Analyse makromolekularer Strukturen und zeigt, wie in der Arzneimittelforschung und -entwicklung die Bioinformatik bestimmte Prozesse noch beschleunigen kann. Zusammenfassung Structural Bioinformatics was the first major effort to show the application of the principles and basic knowledge of the larger field of bioinformatics to questions focusing on macromolecular structure. Inhaltsverzeichnis Foreword xi Preface xv Acknowledgments xix Contributors xxi Section I Data Collection, Analysis, and Visualization 1 1 Defining Bioinformatics and Structural Bioinformatics 3 Russ B. Altman and Jonathan M. Dugan 2 Fundamentals of Protein Structure 15 Eric D. Scheeff and J. Lynn Fink 3 Fundamentals of DNA and RNA Structure 41 Stephen Neidle, Bohdan Schneider, and Helen M. Berman 4 Computational Aspects of High-throughput Crystallographic Macromolecular StructureDetermination 77 Paul D. Adams, Ralf W. Grosse-Kunstleve, and Axel T. Brunger 5 Macromolecular Structure Determination by NMR Spectroscopy 93 John L. Markley, Arash Bahrami, Hamid R. Eghbalnia, Francis C. Peterson, Robert C. Tyler, Eldon L. Ulrich, William M. Westler, and Brian F. Volkman 6 Electron Microscopy in the Context of Structural Systems Biology 143 Niels Volkmann and Dorit Hanein 7 Study of Protein Three-dimensional Structure and Dynamics Using Peptide Amide Hydrogen/Deuterium Exchange Mass Spectrometry (DXMS) and Chemical Cross-linking with Mass Spectrometryto Constrain Molecular Modeling 171 Sheng Li, Dmitri Mouradov, Gordon King, Tong Liu, Ian Ross, Bostjan Kobe, Virgil L. Woods Jr, and Thomas Huber 8 Search and Sampling in Structural Bioinformatics 207 Ilan Samish 9 Molecular Visualization 237 Steven Bottomley and Erik Helmerhorst Section II Data Representation and Databases 269 10 The PDB FORMAT, mmCIF Formats, and Other Data Formats 271 John D. Westbrook and Paula M.D. Fitzgerald 11 The Worldwide Protein Data Bank 293 Helen M. Berman, Kim Henrick, Haruki Nakamura, and John L. Markley 12 The Nucleic Acid Database 305 Bohdan Schneider, Joanna de la Cruz, Zukang Feng, Li Chen, Shuchismita Dutta, Irina Persikova, John D. Westbrook, Huanwang Yang, Jasmine Young, Christine Zardecki, and Helen M. Berman 13 Other Structure-based Databases 321 J. Lynn Fink, Helge Weissig, and Philip E. Bourne Section III Data Integrity and Comparative Features 339 14 Structural Quality Assurance 341 Roman A. Laskowski 15 The Impact of Local Accuracy in Protein and RNA Structures: Validation as an Active Tool 377 Jane S. Richardson and David C. Richardson 16 Structure Comparison and Alignment 397 Marc A. Marti-Renom, Emidio Capriotti, Ilya N. Shindyalov, and Philip E. Bourne 17 Protein Structure Evolution and the SCOP Database 419 Raghu P. R. Metpally and Boojala V. B. Reddy 18 the Cath Domain Structure Database 433 Frances M. G. Pearl, Alison...

List of contents

Foreword.
 

Preface.
 
Acknowledgments.
 
Contributors.
 
Section I DATA COLLECTION, ANALYSIS, AND VISUALIZATION.
 
1 DEFINING BIOINFORMATICS AND STRUCTURAL BIOINFORMATICS (Russ B. Altman and Jonathan M. Dugan).
 
2 FUNDAMENTALS OF PROTEIN STRUCTURE (Eric D. Scheeff and J. Lynn Fink).
 
3 FUNDAMENTALS OF DNA AND RNA STRUCTURE (Stephen Neidle, Bohdan Schneider, and Helen M. Berman).
 
4 COMPUTATIONAL ASPECTS OF HIGH-THROUGHPUT CRYSTALLOGRAPHIC MACROMOLECULAR STRUCTURE DETERMINATION (Paul D. Adams, Ralf W. Grosse-Kunstleve, and Axel T. Brunger).
 
5 MACROMOLECULAR STRUCTURE DETERMINATION BY NMR SPECTROSCOPY (John L. Markley, Arash Bahrami, Hamid R. Eghbalnia, Francis C. Peterson, Robert C. Tyler, Eldon L. Ulrich, William M. Westler, and Brian F. Volkman).
 
6 ELECTRON MICROSCOPY IN THE CONTEXT OF STRUCTURAL SYSTEMS BIOLOGY (Niels Volkmann and Dorit Hanein).
 
7 STUDY OF PROTEIN THREE-DIMENSIONAL STRUCTURE AND DYNAMICS USING PEPTIDE AMIDE HYDROGEN/ DEUTERIUM EXCHANGE MASS SPECTROMETRY (DXMS) AND CHEMICAL CROSS-LINKING WITH MASS SPECTROMETRY TO CONSTRAIN MOLECULAR MODELING (Sheng Li, Dmitri Mouradov, Gordon King, Tong Liu, Ian Ross, Bostjan Kobe, Virgil L. Woods Jr, and Thomas Huber).
 
8 SEARCH AND SAMPLING IN STRUCTURAL BIOINFORMATICS (Ilan Samish).
 
9 MOLECULAR VISUALIZATION (Steven Bottomley and Erik Helmerhorst).
 
Section II DATA REPRESENTATION AND DATABASES.
 
10 THE PDB FORMAT, mmCIF FORMATS, AND OTHER DATA FORMATS (John D. Westbrook and Paula M.D. Fitzgerald).
 
11 THE WORLDWIDE PROTEIN DATA BANK (Helen M. Berman, Kim Henrick, Haruki Nakamura, and John L. Markley).
 
12 THE NUCLEIC ACID DATABASE (Bohdan Schneider, Joanna de la Cruz, Zukang Feng, Li Chen, Shuchismita Dutta, Irina Persikova, John D. Westbrook, Huanwang Yang, Jasmine Young, Christine Zardecki, and Helen M. Berman).
 
13 OTHER STRUCTURE-BASED DATABASES (J. Lynn Fink, Helge Weissig, and Philip E. Bourne).
 
Section III DATA INTEGRITY AND COMPARATIVE FEATURES.
 
14 STRUCTURAL QUALITY ASSURANCE (Roman A. Laskowski).
 
15 THE IMPACT OF LOCAL ACCURACY IN PROTEIN AND RNA STRUCTURES: VALIDATION AS AN ACTIVE TOOL (Jane S. Richardson and David C. Richardson).
 
16 STRUCTURE COMPARISON AND ALIGNMENT (Marc A. Marti-Renom, Emidio Capriotti, Ilya N. Shindyalov, and Philip E. Bourne).
 
17 PROTEIN STRUCTURE EVOLUTION AND THE SCOP DATABASE (Raghu P. R. Metpally and Boojala V. B. Reddy).
 
18 THE CATH DOMAIN STRUCTURE DATABASE (Frances M. G. Pearl, Alison Cuff, and Christine A. Orengo).
 
Section IV STRUCTURAL AND FUNCTIONAL ASSIGNMENT.
 
19 SECONDARY STRUCTURE ASSIGNMENT (Claus A. Andersen and Burkhard Rost).
 
20 IDENTIFYING STRUCTURAL DOMAINS IN PROTEINS (Stella Veretnik, Jenny Gu, and Shoshana Wodak).
 
21 INFERRING PROTEIN FUNCTION FROM STRUCTURE (James D. Watson, Gail J. Bartlett, and Janet M. Thornton).
 
22 STRUCTURAL ANNOTATION OF GENOMES (Adam J. Reid, Corin Yeats, Jonathan Lees, and Christine A. Orengo).
 
23 EVOLUTION STUDIED USING PROTEIN STRUCTURE (Song Yang, Ruben Valas, and Philip E. Bourne).
 
Section V MACROMOLECULAR INTERACTIONS.
 
24 ELECTROSTATIC INTERACTIONS (Nathan A. Baker and J. Andrew McCammon).
 
25 PREDICTION OF PROTEIN-NUCLEIC ACID INTERACTIONS (Timothy Robertson and Gabriele Varani).
 
26 PREDICTION OF PROTEIN-PROTEIN INTERACTIONS FROM EVOLUTIONARY INFORMATION (Alfonso Valencia and Florencio Pazos).
 
27 DOCKING METHODS, LIGAND DESIGN, AND VALIDATING DATA SETS IN THE STRUCTURAL GENOMICS ERA (Natasja Brooijmans).
 
Section VI STRUCTURE PREDICTION.
 
28 CASP AND OTHER COMMUNITY-WIDE ASSESSMENTS TO ADVANCE THE FIELD OF STRUCTURE PREDICTION (Jen

Report

"Offering a detailed coverage for practitioners but remaining accessible to the novice, Structural Bioinformatics, Second Edition is a valuable and excellent textbook for readers in the bioinformatics and advanced biology fields, and on the best way to become a classic reference for all interested parties (educators, researchers and graduate students.)" (Advances in Food Sciences, 2011)

Product details

• Authors: Jenny Bourne Gu, GU JENNY BOURNE PHILIP E
• Assisted by: Philip E Bourne (Editor), Philip E. Bourne (Editor), Bourne Philip E. (Editor), E Bourne (Editor), Jenny Gu (Editor), Gu Jenny (Editor)
• Publisher: Wiley, John and Sons Ltd
• Languages: English
• Product format: Hardback
• Released: 03.04.2009
• EAN: 9780470181058
• ISBN: 978-0-470-18105-8
• No. of pages: 1104
• Subjects: Natural sciences, medicine, IT, technology > Biology > General, dictionaries; Chemie, Bioinformatik, Life Sciences, Biowissenschaften, chemistry, Pharmaceutical & Medicinal Chemistry, Pharmazeutische u. Medizinische Chemie, Bioinformatics & Computational Biology, Genomforschung u. Proteomik, Genomics & Proteomics