Assessment of novel fold targets in CASP4: Predictions of three-dimensional structures, secondary structures, and interresidue contacts

Authors

  • Arthur M. Lesk,

    Corresponding author
    1. Department of Haematology, University of Cambridge Clinical School, Cambridge Institute for Medical Research, Cambridge, United Kingdom
    • Department of Haematology, University of Cambridge Clinical School, Cambridge Institute for Medical Research, Wellcome/MRC Building, Hills Road, Cambridge CB2 2XY, United Kingdom
    Search for more papers by this author
  • Loredana Lo Conte,

    1. MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    Search for more papers by this author
  • Tim J.P. Hubbard

    1. The Sanger Centre Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
    Search for more papers by this author

Abstract

In the Novel Fold category, three types of predictions were assessed: three-dimensional structures, secondary structures, and residue-residue contacts. For predictions of three-dimensional models, CASP4 targets included 5 domains or structures with novel folds, and 13 on the borderline between Novel Fold and Fold Recognition categories. These elicited 1863 predictions of these and other targets by methods more general than comparative modeling or fold recognition techniques. The group of Bonneau, Tsai, Ruczinski, and Baker stood out as performing well with the greatest consistency. In many cases, several groups were able to predict fragments of the target correctly—often at a level somewhat larger than standard supersecondary structures—but were not able to assemble fragments into a correct global topology. The methods of Bonneau, Tsai, Ruczinski, and Baker have been successful in addressing the fragment assembly problem for many but not all the target structures. Proteins 2001;Suppl 5:98–118. © 2002 Wiley-Liss, Inc.

Ancillary