Protein fold recognition by mapping predicted secondary structures

Robert B. Russell, Richard R. Copley and Geoffrey J. Barton

University of Oxford
Laboratory of Molecular Biophysics
The Rex Richards Building, South Parks Road
Oxford, OX1 3QU, England
Tel: 44 1865 275368 FAX: 44 1865 510454
E-mail: gjb@bioch.ox.ac.uk

Present Address:
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund Laboratories
44 Lincoln's Inn Fields, P.O. Box 123
London, WC2A 3PX, England
E-mail: russell@icrf.icnet.uk

To whom correspondence should be addressed.

Keywords: protein; structure prediction; fold recognition; threading; nuclear magnetic resonance; secondary structure mapping.

Running title: Fold recognition from secondary structure prediction

Published in J. Mol. Biol. (1996), 259, (3), 349-365.

• Contents
• abstract
• Introduction
• Methods
  • Database of unique protein 3D structural domains
  • Alignment of secondary structures
  • Filters
    • Removing un-compact structures
    • Loop length distance restraints
    • Poor sheets
    • Adjacent parallel structures
    • Distance restraints
    • Consistency &Redundancy
    • Maps removed by each filter
  • Fitting sequences on to 3D structures
  • Protein Structure Patterns for Evaluation
  • Cross-validation
  • Computational details
• Results
  • Assessing accuracy
  • Searches with eleven test proteins
  • Fold recognition from published predictions
    • The vWF domain
    • The Proteasome
    • The phosphotyrosine interaction domain
• Discussion &Conclusions
• Acknowledgements
• Abbreviations
• Figure and Table Legends
  • Figure 1
  • Figure 2
  • Figure 3
  • Table 6
  • Table 7
• Figures
• Tables
• References
• About this document ...