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References
RAPTOR has been developed based on the techniques described in following papers. RAPTOR ranks first among all non-meta servers in CAFASP3 (Third Critical Assessment of Fully Automated Structure Prediction), an absolutely blind test of structure prediction servers organized by the protein structure prediction community. RAPTOR also ranks third among all non-meta servers in CASP6 according to http://www.bioinformatics.buffalo.edu/casp6/
Jinbo Xu. Protein Structure Prediction by Linear Programming, University of Waterloo, August 2003. [ps] [pdf]
Jinbo Xu, Ying Xu, Dongsup Kim, Ming Li. RAPTOR: Optimal Protein Threading by Linear Programming, the inaugural issue, Journal of Bioinformatics and Computational Biology, April 2003.[pdf] [ps]
Jinbo Xu, Ying Xu, Guohui Lin, Dongsup Kim, Ming Li. Protein Structure
Prediction By Linear Programming, Pacific Symposium Biocomputing 2003.[ps][pdf]
Jinbo Xu, Ming Li. Assessment of RAPTOR's linear programming approach in
CAFASP3, CASP5 (Fifth Critical Assessment of Structure Prediction) special
issue, Proteins: Structure, Function and Genetics. Oct, 2003. [ps][pdf]
Note: This is an invited paper, the only one voted by all the CASP5/CAFASP3
attendees according to the novelty and performance.
Jinbo Xu. Protein Fold Recognition by Predicted Alignment Accuracy. IEEE/ACM Trans. on Computational Biology and Bioinformatics.[ps] [pdf]
Jinbo Xu, Ying Xu, Ming Li. Protein Threading by Linear Programming:
Theoretical Analysis and Computational Results, Journal of Combinatorial
Optimization, 2004. In Press.[ps][pdf]
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