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
