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 h...

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Bibliographic Details
Main Author: Jenny Gu; Philip E Bourne
Format: Printed Book
Published: New Jersey Wiley-Blackwell 2009
Edition:2nd edition
Subjects:
Structural bioinformatics. Computational Biology. Molecular Biology.
Table of Contents:
  • 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.

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