| Formatted contents note |
Data Collection, Analysis, and Visualization -- Defining Bioinformatics and Structural Bioinformatics / Russ B. Altman, Jonathan M. Dugan -- Fundamentals of Protein Structure / Eric D. Scheef, J. Lynn Fink -- Fundamentals of DNA and RNA Structure / Stephen Neidle, Bohdan Schneider, Helen M. Berman -- Computational Aspects of High-Throughput Crystallographic Macromolecular Structure Determination / Paul D. Adams, Ralf W. Grosse-Kunstleve, Axel T. Brunger -- 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, Brian F. Volkman -- Electron Microscopy in the Context of Structural Systems Biology / Niels Volkmann, Dorit Hanein -- 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., Thomas Huber -- Search and Sampling in Structural Bioinformatics / Han Samish -- Molecular Visualization / Steven Bottomley, Erik Helmerhorst. Data representation and databases -- The PDB Format, mmCIF Formats, and Other Data Formats / John D. Westbrook, Paula M.D. Fitzgerald -- The Worldwide Protein Data Bank / Helen M. Berman, Kim Henrick, Haruki Nakamura, John L. Markley -- 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, Helen M. Berman -- Other Structure-Based Databases / J. Lynn Fink, Helge Weissig, and Philip E. Bourne. Data integrity and comparative features -- Structural Quality Assurance / Roman A. Laskowski -- The Impact of Local Accuracy in Protein and RNA Structures: Validation as an Active Tool / Jane S. Richardson, David C. Richardson -- Structure Comparison and Alignment / Marc A. Marti-Renom, Emidio Capriotti, Ilya N. Shindyalov, Philip E. Bourne -- Protein Structure Evolution and the SCOP Database / Raghu P.R. Metpally, Boojala V.B. Reddy -- The CATH Domain Structure Database / Frances M.G. Pearl, Alison Cuff, Christine A. Orengo. Structural and functional assignment -- Secondary Structure Assignment / Claus A. Andersen, Burkhard Rost -- Identifying Structural Domains in Proteins / Stella Veretnik, Jenny Gu, Shoshana Wodak -- Inferring Protein Function from Structure / James D. Watson, Gail J. Bartlett, Janet M. Thornton -- Structural Annotation of Genomes / Adam J. Reid, Corin Yeats, Jonathan Lees, Christine A. Orengo -- Evolution Studied Using Protein Structure / Song Yang, Ruben Valas, Philip E. Bourne. Macromolecular interactions -- Electrostatic Interactions / Nathan A. Baker, J. Andrew McCammon -- Prediction of Protein-Nucleic Acid Interactions / Timothy Robertson, Gabriele Varani -- Prediction of Protein-Protein Interactions from Evolutionary Information / Alfonso Valencia, Florencio Pazos -- Docking Methods, Ligand Design, and Validating Data Sets in the Structural Genomics Era / Natasja Brooijmans. Structure prediction -- CASP and Other Community-Wide Assessments to Advance the Field of Structure Prediction / Jenny Gu, Philip E. Bourne -- Prediction of Protein Structure in 1D: Secondary Structure, Membrane Regions, and Solvent Accessibility / Burkhard Rost -- Homology Modeling / Hanka Venselaar, Elmar Krieger, Gert Vriend -- Fold Recognition Methods / Adam Godzik -- De Novo Protein Structure Prediction: Methods and Application / Kevin Drew, Dylan Chivian, Richard Bonneau -- RNA Structural Bioinformatics / Magdalena A. Jonikas, Alain Laederach, Russ B. Altman. Therapeutic discovery -- Structural Bioinformatics in Drug Discovery / William R. Pitt, Alicia Perez Higueruelo, Colin R. Groom -- B-Cell Epitope Prediction / Julia V. Ponomarenko, Marc H.V. van Regenmortel. Future Challenges -- Methods to Classify and Predict the Structure of Membrane Proteins / Marialuisa Pellegrini-Calace, Janet M. Thornton -- Protein Motion: Simulation / Ilan Samish, Jenny Gu, Michael L. Klein -- The Significance and Impacts of Protein Disorder and Conformational Variants / Jenny Gu, Vincent J. Hilser -- Protein Designability and Engineering / Nikolay V. Dokholyan -- Structural Genomics of Protein Superfamilies / Stephen K. Burley, Steven C. Almo, Jeffrey B. Bonanno -- Mark R. Chance, Spencer Emtage, Andras Fiser, Andrej Sali, J. Michael Sauder, Subramanyam Swaminathan. |
