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New Fold Methods: Prediction Reports
Predicting interresidue contacts using templates and pathways
Article first published online: 15 OCT 2003
DOI: 10.1002/prot.10539
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 497–502, 2003
Additional Information
How to Cite
Shao, Y. and Bystroff, C. (2003), Predicting interresidue contacts using templates and pathways. Proteins, 53: 497–502. doi: 10.1002/prot.10539
Publication History
- Issue published online: 15 OCT 2003
- Article first published online: 15 OCT 2003
- Manuscript Accepted: 19 MAY 2003
- Manuscript Received: 13 FEB 2003
- Abstract
- Article
- References
- Cited By
Keywords:
- predictions;
- contact maps;
- HMMSTR;
- rule-based;
- protein folding;
- I-sites;
- Rosetta;
- hidden Markov models
Abstract
We present a novel method, HMMSTR-CM, for protein contact map predictions. Contact potentials were calculated by using HMMSTR, a hidden Markov model for local sequence structure correlations. Targets were aligned against protein templates using a Bayesian method, and contact maps were generated by using these alignments. Contact potentials then were used to evaluate these templates. An ab initio method based on the target contact potentials using a rule-based strategy to model the protein-folding pathway was developed. Fold recognition and ab initio methods were combined to produce accurate, protein-like contact maps. Pathways sometimes led to an unambiguous prediction of topology, even without using templates. The results on CASP5 targets are discussed. Also included is a brief update on the quality of fully automated ab initio predictions using the I-sites server. Proteins 2003;53:497–502. © 2003 Wiley-Liss, Inc.