Structural Bioinformatics

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, such as the prediction of protein structure and how proteins carry out cellular functions, and how the application of bioinformatics to these life science issues can improve healthcare by accelerating drug discovery and development. Designed primarily as a reference, the first edition nevertheless saw widespread use as a textbook in graduate and undergraduate university courses dealing with the theories and associated algorithms, resources, and tools used in the analysis, prediction, and theoretical underpinnings of DNA, RNA, and proteins. This new edition contains not only thorough updates of the advances in structural bioinformatics since publication of the first edition, but also features eleven new chapters dealing with frontier areas of high scientific impact, including: sampling and search techniques; use of mass spectrometry; genome functional annotation; and much more. Offering detailed coverage for practitioners while remaining accessible to the novice, Structural Bioinformatics, Second Edition is a valuable resource and an excellent textbook for a range of readers in the bioinformatics and advanced biology fields. Praise for the previous edition: "This book is a gold mine of fundamental and practical information in an area not previously well represented in book form." —Biochemistry and Molecular Education "... destined to become a classic reference work for workers at all levels in structural bioinformatics...recommended with great enthusiasm for educators, researchers, and graduate students." —BAMBED "...a useful and timely summary of a rapidly expanding field." —Nature Structural Biology "...a terrific job in this timely creation of a compilation of articles that appropriately addresses this issue." —Briefings in Bioinformatics

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.

Review :
"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)