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New Fold Methods: Prediction Reports
Assembling novel protein folds from super-secondary structural fragments
Article first published online: 15 OCT 2003
DOI: 10.1002/prot.10542
Copyright © 2003 Wiley-Liss, Inc.
Issue
1097-0134/asset/cover.gif?v=1&s=d817e79b67ba6cacf8bdcce1a819c04de300a7e3 "Proteins: Structure, Function, and Bioinformatics")
Proteins: Structure, Function, and Bioinformatics
Supplement: Fifth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction
Volume 53, Issue Supplement 6, pages 480–485, 2003
Additional Information
How to Cite
Jones, D. T. and McGuffin, L. J. (2003), Assembling novel protein folds from super-secondary structural fragments. Proteins, 53: 480–485. doi: 10.1002/prot.10542
Publication History
- Issue published online: 15 OCT 2003
- Article first published online: 15 OCT 2003
- Manuscript Accepted: 3 APR 2003
- Manuscript Received: 17 FEB 2003
- Abstract
- Article
- References
- Cited By
Keywords:
- protein structure prediction;
- folding;
- simulation;
- novel folds;
- fold recognition
Abstract
The results of applying a fragment-based protein tertiary structure prediction method to the prediction of 14 CASP5 target domains are described. The method is based on the assembly of supersecondary structural fragments taken from highly resolved protein structures using a simulated annealing algorithm. A number of good predictions for proteins with novel folds were produced, although not always as the first model. For two fold recognition targets, FRAGFOLD produced the most accurate model in both cases, despite the fact that the predictions were not based on a template structure. Although clear progress has been made in improving FRAGFOLD since CASP4, the ranking of final models still seems to be the main problem that needs to be addressed before the next CASP experiment. Proteins 2003;53:480–485. © 2003 Wiley-Liss, Inc.