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R?Hpred: Prediction of Right-Handed ?-Helix Fold from Protein Sequence Using SVM and Protein Threading
Aizu-Wakamatsu City, Fukushima, Japan October 16-October 19
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/CIT.2007.757th IEEE International Conference on ...
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Siddharth Singh, Krishnan Hajela, Ashwini Ramani, "R?Hpred: Prediction of Right-Handed ?-Helix Fold from Protein Sequence Using SVM and Protein Threading," Computer and Information Technology, International Conference on, pp. 1116-1121, 7th IEEE International Conference on Computer and Information Technology (CIT 2007), 2007.
 
 
BibTex
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@article{ 10.1109/CIT.2007.75,
author = {Siddharth Singh and Krishnan Hajela and Ashwini Ramani},
title = {R?Hpred: Prediction of Right-Handed ?-Helix Fold from Protein Sequence Using SVM and Protein Threading},
journal ={Computer and Information Technology, International Conference on},
volume = {0},
year = {2007},
isbn = {0-7695-2983-6},
pages = {1116-1121},
doi = {http://doi.ieeecomputersociety.org/10.1109/CIT.2007.75},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - CONF
JO - Computer and Information Technology, International Conference on
TI - R?Hpred: Prediction of Right-Handed ?-Helix Fold from Protein Sequence Using SVM and Protein Threading
SN - 0-7695-2983-6
SP1116
EP1121
A1 - Siddharth Singh,
A1 - Krishnan Hajela,
A1 - Ashwini Ramani,
PY - 2007
VL - 0
JA - Computer and Information Technology, International Conference on
ER -
 
Siddharth Singh, Devi Ahilya University, Indore, India
Krishnan Hajela, Devi Ahilya University, Indore, India
Ashwini Ramani, Devi Ahilya University, Indore, India
The right-handed single-stranded helix proteins characterized as virulence factors, allergens and toxins are threat to human health. Identification of these proteins from primary sequence is of great importance in bio-medicine and medical microbiology. In this paper, support vector machine (SVM) has been used to predict the presence of ?-helix fold in protein sequences using dipeptide composition. Input vector of 400 dimensions is used to search for the presence of conserved secondary structure called rungs in ?-helix proteins. A maximum accuracy of 90.1% and Matthew's correlation coefficient of 0.77 is obtained in a 5-fold cross-validation procedure. In addition, a position specific scoring matrix(PSSM) is also used to score putative rung sequences identified by SVM. Finally, the predicted ?-helix proteins are threaded against a custom ?-helix template library to achieve high prediction confidence. The method recognizes right-handed ?-helices with 100% sensitivity and 99.8% specificity on a test set of known protein structures.
Citation:
Siddharth Singh, Krishnan Hajela, Ashwini Ramani, "R?Hpred: Prediction of Right-Handed ?-Helix Fold from Protein Sequence Using SVM and Protein Threading," cit, pp.1116-1121, 7th IEEE International Conference on Computer and Information Technology (CIT 2007), 2007
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