Structural Bioinformatics
Editors: Phil Bourne and Helge Weissig

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    "Just a quick message to thank you for putting together a great book on structural bioinformatics. I think it is a very timely publication given the growing interest in the 'functional' aspects of genomics and structure-based drug design. We will recommend the book to our third year Molecular Genetics students who take a unit in structural bioinformatics in the final semester of their undergraduate degree."

    Steve Bottomley, Curtin University of Technology, Australia

    "I am a protein crystallographer and I am teaching protein engineering and bioinformatics to our graduate students. Recently I have seen in the e.mail that you have published a book on structural bioinformatics. I hav seen the chapters in the aamazon.com and it is very interesting to note the topics. Exactly the same thing I want to teach our students."

    Amit Kumar Das, Department of Biotechnology, Indian Institute of Technology, India
Chapter Outline:
  i. Preface by John Wooley, University of California, San Diego
  ii. Introductory Comments by the Editors
  Section I - Introduction
  1. What is Bioinformatics and Structural Bioinformatics?
Russ Altman and Jon Dugan, Stanford University
  2. Fundamentals of Protein Structure
Eric Scheeff and Lynn Fink, University of California San Diego
  3. Fundamentals of DNA and RNA Structure
Helen Berman, Bohdan Schneider and Stephen Needle, Rutgers University
  4. Computational Aspects of High-throughput Crystallographic Macromolecular Structure Determination
Paul Adams, Ralf Grosse-Kunstleve and Axel Brunger, Stanford University
  5. Macromolecular Structure Determination by NMR
John Markley, Eldon Ulrich, and Brian Volkman, University of Wisconsin
  6. Electron Microscopy
Niels Volkman, The Burnham Institute
  7. Molecular Visualization
John Tate, European Biotechnology Institute
  Section II - Data Representation and Databases
  8. The PDB Format, mmCIF Formats and Other Data Formats
John Westbrook, Rutgers University and Paula Fitzgerald Merck Pharmaceuticals Inc.
  9. The Protein Data Bank
The Research Collaboratory for Structural Bioinformatics
  10. The Nucleic Acid Database
Helen Berman and John Westbrook, Rutgers University
  11. Other Structure Based Databases
Helge Weissig and Philip Bourne, University of California San Diego
  Section III - Comparative Features
  12. The Structure Classification of Proteins (SCOP)
Boojla Reddy and Philip Bourne, University of California San Diego
  13. Class, Architecture, Topology, Homology (CATH) Classification
Christine Orengo, University College London
  14. Stereochemical Quality and Structure Assignments
Roman Laskowski, University College London
  15. All-Atom Contacts: A New Approach to Structure Validation
Jane Richardson, Duke University
  16. Structure-structure Comparison and Alignment
Ilya Shindyalov and Philip Bourne, University of California San Diego
  Section IV - Structure and Functional Assignment
  17. Automated Secondary Structure Assignment
Claus Andersen and Burkhard Rost, Columbia University
  18. Domain Assignments
Lorenz Wernisch and Shoshana Wodak, EBI/EMBL & The Free University Brussels
  19. Infering Function from Structure
Gail Bartlett, Annabel Todd and Janet Thornton, University College London
  Section V - Protein Interactions
  20. Prediction Of Protein Structure And Protein Interaction From Evolutionary Information
Alfonso Valencia and Florencio Pazos, Protein Design Group, CNB-CSIC
  21. Electrostatic Interactions
Nathan Baker and Andrew McCammon, University of California San Diego
  Section VI - Proteins as Drug Targets
  22. Docking and Ligand Design
J. Krumrine, F. Raubacher, N. Brooijmans, and I. Kuntz , University of California San Francisco.
  23. The Drug Discovery Process
Eric Fauman, Colin Groom and Andrew Hopkins, Pfizer Pharmaceuticals
  Section VII - Structure Prediction
  24. The CASP Experiment and its Findings
Phil Bourne, University of California
  25. Homology Modeling
Elmar Krieger and Gert Vriend, University of Nijmegen
  26. Fold Recognition Methods
Adam Godzik, The Burnham Institute
  27. Ab initio Methods
Dylan Chivian and David Baker, University of Washington
  28. Prediction in 1D: Secondary Structure, Membrane Helices, and Accessibility
Burkhard Rost, Columbia University
  Section VIII - The Future
  29. Structural Genomics
Steven Burley, The Rockefeller University
  30. Epilogue