1097-0134/asset/PROT_centre.gif?v=1&s=77b56b1f2cdaba74cb3bb149bd9b029cd8803cdb)
New Methods
Assessment of RAPTOR's linear programming approach in CAFASP3
Article first published online: 15 OCT 2003
DOI: 10.1002/prot.10531
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 579–584, 2003
Additional Information
How to Cite
Xu, J. and Li, M. (2003), Assessment of RAPTOR's linear programming approach in CAFASP3. Proteins, 53: 579–584. doi: 10.1002/prot.10531
Publication History
- Issue published online: 15 OCT 2003
- Article first published online: 15 OCT 2003
- Manuscript Accepted: 7 MAY 2003
- Manuscript Received: 14 MAR 2003
- Abstract
- Article
- References
- Cited By
Keywords:
- protein threading;
- integer programming;
- support vector machines
Abstract
We have developed a new algorithm based on the mathematical theory of linear programming (LP) and implemented it in our program RAPTOR. Our new approach provides an elegant formulation of the protein-threading problem, overcomes the intractability problem of protein threading, in practice, and allows us to use existing powerful linear programming software to obtain optimal protein threading solutions. CASP5 and CAFASP3 gave us the first chance to test RAPTOR in an unbiased way. RAPTOR was ranked as the top individual (automatic) server for fold recognition by the CAFASP3 organizers. In this short article, we describe RAPTOR's LP formulation, assess RAPTOR's performance in CAFASP3/CASP5, explain why it has superceded other existing automatic individual methods, and point out its strengths, limitations, extensions, and prospects for improvement. Proteins 2003;53:579–584. © 2003 Wiley-Liss, Inc.