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Prediction of the protein structural class by specific peptide frequencies.

Authors :
Costantini S
Facchiano AM
Source :
Biochimie [Biochimie] 2009 Feb; Vol. 91 (2), pp. 226-9. Date of Electronic Publication: 2008 Oct 10.
Publication Year :
2009

Abstract

We evaluated the i-peptides occurrence frequency in the protein sequences belonging to the two datasets which include proteins with a sequence similarity lower than 25% and 40%, respectively. We worked out a new structural class prediction algorithm using the most frequent i-peptides (with i=2, 3, 4), which characterize the four structural classes. Using the tri-peptides, much more able to gain structural information from sequences compared to the di-peptides, the best results were obtained. Compared to the other methods, similarly founded on peptide occurrence frequencies, our method achieves the best prediction accuracy. We compared it also with methods founded on more sophisticated computational approaches.

Details

Language :
English
ISSN :
1638-6183
Volume :
91
Issue :
2
Database :
MEDLINE
Journal :
Biochimie
Publication Type :
Academic Journal
Accession number :
18957316
Full Text :
https://doi.org/10.1016/j.biochi.2008.09.005