Table of Contents

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 Cuff, and Christine A. Orengo

Section IV Structural and Functional Assignment 457

19 Secondary Structure Assignment 459
Claus A. Andersen and Burkhard Rost

20 Identifying Structural Domains in Proteins 485
Stella Veretnik, Jenny Gu, and Shoshana Wodak

21 Inferring Protein Function From Structure 515
James D. Watson, Gail J. Bartlett, and Janet M. Thornton

22 Structural Annotation of Genomes 539
Adam J. Reid, Corin Yeats, Jonathan Lees, and Christine A. Orengo

23 Evolution Studied Using Protein Structure 559
Song Yang, Ruben Valas, and Philip E. Bourne

Section V Macromolecular Interactions 573

24 Electrostatic Interactions 575
Nathan A. Baker and J. Andrew McCammon

25 Prediction of Protein–nucleic Acid Interactions 593
Timothy Robertson and Gabriele Varani

26 Prediction of Protein–protein Interactions From Evolutionary Information 615
Alfonso Valencia and Florencio Pazos

27 Docking Methods, Ligand Design, and Validating Data Sets in the Structural Genomics Era 633
Natasja Brooijmans

Section VI Structure Prediction 663

28 CASP and other Community-wide Assessments to Advance the Field Of Structure Prediction 665
Jenny Gu and Philip E. Bourne

29 Prediction of Protein Structure in 1d: Secondary Structure, Membrane Regions, and SolventAccessibility 679
Burkhard Rost

30 Homology Modeling 715
Hanka Venselaar, Elmar Krieger, and Gert Vriend

31 Fold Recognition Methods 733
Adam Godzik

32 De Novo Protein Structure Prediction: Methods and Application 755
Kevin Drew, Dylan Chivian, and Richard Bonneau

33 Rna Structural Bioinformatics 791
Magdalena A. Jonikas, Alain Laederach, and Russ B. Altman

Section VII Therapeutic Discovery 807

34 Structural Bioinformatics in Drug Discovery 809
William R. Pitt, Alícia Perez Higueruelo, and Colin R. Groom

35 B-cell Epitope Prediction 847
Julia V. Ponomarenko and Marc H.V. van Regenmortel

Section VIII Future Challenges 879

36 Methods to Classify and Predict the Structure of Membrane Proteins 881
Marialuisa Pellegrini-Calace and Janet M. Thornton

37 Protein Motion: Simulation 907
Ilan Samish, Jenny Gu, and Michael L. Klein

38 The Significance and Impacts of Protein Disorder and Conformational Variants 937
Jenny Gu and Vincent J. Hilser

39 Protein Designability and Engineering 961
Nikolay V. Dokholyan

40 Structural Genomics of Protein Superfamilies 983
Stephen K. Burley, Steven C. Almo, Jeffrey B. Bonanno, Mark R. Chance, Spencer Emtage, Andras Fiser, Andrej Sali, J. Michael Sauder, and Subramanyam Swaminathan

Index 1019

About the Author

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.

Reviews

"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)