Structural Bioinformatics

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.

"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)

• Foreword xiPreface xvAcknowledgments xixContributors xxiSection I Data Collection, Analysis, and Visualization 11 Defining Bioinformatics and Structural Bioinformatics 3Russ B. Altman and Jonathan M. Dugan2 Fundamentals of Protein Structure 15Eric D. Scheeff and J. Lynn Fink3 Fundamentals of DNA and RNA Structure 41Stephen Neidle, Bohdan Schneider, and Helen M. Berman4 Computational Aspects of High-throughput Crystallographic Macromolecular StructureDetermination 77Paul D. Adams, Ralf W. Grosse-Kunstleve, and Axel T. Brunger5 Macromolecular Structure Determination by NMR Spectroscopy 93John L. Markley, Arash Bahrami, Hamid R. Eghbalnia, Francis C. Peterson, Robert C. Tyler, Eldon L. Ulrich, William M. Westler, and Brian F. Volkman6 Electron Microscopy in the Context of Structural Systems Biology 143Niels Volkmann and Dorit Hanein7 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 171Sheng Li, Dmitri Mouradov, Gordon King, Tong Liu, Ian Ross, Bostjan Kobe, Virgil L. Woods Jr, and Thomas Huber8 Search and Sampling in Structural Bioinformatics 207Ilan Samish9 Molecular Visualization 237Steven Bottomley and Erik HelmerhorstSection II Data Representation and Databases 26910 The PDB FORMAT, mmCIF Formats, and Other Data Formats 271John D. Westbrook and Paula M.D. Fitzgerald11 The Worldwide Protein Data Bank 293Helen M. Berman, Kim Henrick, Haruki Nakamura, and John L. Markley12 The Nucleic Acid Database 305Bohdan 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. Berman13 Other Structure-based Databases 321J. Lynn Fink, Helge Weissig, and Philip E. BourneSection III Data Integrity and Comparative Features 33914 Structural Quality Assurance 341Roman A. Laskowski15 The Impact of Local Accuracy in Protein and RNA Structures: Validation as an Active Tool 377Jane S. Richardson and David C. Richardson16 Structure Comparison and Alignment 397Marc A. Marti-Renom, Emidio Capriotti, Ilya N. Shindyalov, and Philip E. Bourne17 Protein Structure Evolution and the SCOP Database 419Raghu P. R. Metpally and Boojala V. B. Reddy18 the Cath Domain Structure Database 433Frances M. G. Pearl, Alison Cuff, and Christine A. OrengoSection IV Structural and Functional Assignment 45719 Secondary Structure Assignment 459Claus A. Andersen and Burkhard Rost20 Identifying Structural Domains in Proteins 485Stella Veretnik, Jenny Gu, and Shoshana Wodak21 Inferring Protein Function From Structure 515James D. Watson, Gail J. Bartlett, and Janet M. Thornton22 Structural Annotation of Genomes 539Adam J. Reid, Corin Yeats, Jonathan Lees, and Christine A. Orengo23 Evolution Studied Using Protein Structure 559Song Yang, Ruben Valas, and Philip E. BourneSection V Macromolecular Interactions 57324 Electrostatic Interactions 575Nathan A. Baker and J. Andrew McCammon25 Prediction of Protein–nucleic Acid Interactions 593Timothy Robertson and Gabriele Varani26 Prediction of Protein–protein Interactions From Evolutionary Information 615Alfonso Valencia and Florencio Pazos27 Docking Methods, Ligand Design, and Validating Data Sets in the Structural Genomics Era 633Natasja BrooijmansSection VI Structure Prediction 66328 CASP and other Community-wide Assessments to Advance the Field Of Structure Prediction 665Jenny Gu and Philip E. Bourne29 Prediction of Protein Structure in 1d: Secondary Structure, Membrane Regions, and SolventAccessibility 679Burkhard Rost30 Homology Modeling 715Hanka Venselaar, Elmar Krieger, and Gert Vriend31 Fold Recognition Methods 733Adam Godzik32 De Novo Protein Structure Prediction: Methods and Application 755Kevin Drew, Dylan Chivian, and Richard Bonneau33 Rna Structural Bioinformatics 791Magdalena A. Jonikas, Alain Laederach, and Russ B. AltmanSection VII Therapeutic Discovery 80734 Structural Bioinformatics in Drug Discovery 809William R. Pitt, Alícia Perez Higueruelo, and Colin R. Groom35 B-cell Epitope Prediction 847Julia V. Ponomarenko and Marc H.V. van RegenmortelSection VIII Future Challenges 87936 Methods to Classify and Predict the Structure of Membrane Proteins 881Marialuisa Pellegrini-Calace and Janet M. Thornton37 Protein Motion: Simulation 907Ilan Samish, Jenny Gu, and Michael L. Klein38 The Significance and Impacts of Protein Disorder and Conformational Variants 937Jenny Gu and Vincent J. Hilser39 Protein Designability and Engineering 961Nikolay V. Dokholyan40 Structural Genomics of Protein Superfamilies 983Stephen K. Burley, Steven C. Almo, Jeffrey B. Bonanno, Mark R. Chance, Spencer Emtage, Andras Fiser, Andrej Sali, J. Michael Sauder, and Subramanyam SwaminathanIndex 1019