Oxypred: prediction and classification of oxygen-binding proteins

S Muthukrishnan, A Garg… - Genomics, Proteomics …, 2007 - academic.oup.com
S Muthukrishnan, A Garg, GPS Raghava
Genomics, Proteomics and Bioinformatics, 2007academic.oup.com
This study describes a method for predicting and classifying oxygen-binding proteins. Firstly,
support vector machine (SVM) modules were developed using amino acid composition and
dipeptide composition for predicting oxygen-binding proteins, and achieved maximum
accuracy of 85.5% and 87.8%, respectively. Secondly, an SVM module was developed
based on amino acid composition, classifying the predicted oxygen-binding proteins into six
classes with accuracy of 95.8%, 97.5%, 97.5%, 96.9%, 99.4%, and 96.0% for erythrocruorin …
Abstract
This study describes a method for predicting and classifying oxygen-binding proteins. Firstly, support vector machine (SVM) modules were developed using amino acid composition and dipeptide composition for predicting oxygen-binding proteins, and achieved maximum accuracy of 85.5% and 87.8%, respectively. Secondly, an SVM module was developed based on amino acid composition, classifying the predicted oxygen-binding proteins into six classes with accuracy of 95.8%, 97.5%, 97.5%, 96.9%, 99.4%, and 96.0% for erythrocruorin, hemerythrin, hemocyanin, hemoglobin, leghemoglobin, and myoglobin proteins, respectively. Finally, an SVM module was developed using dipeptide composition for classifying the oxygen-binding proteins, and achieved maximum accuracy of 96.1%, 98.7%, 98.7%, 85.6%, 99.6%, and 93.3% for the above six classes, respectively. All modules were trained and tested by five-fold cross validation. Based on the above approach, a web server Oxypred was developed for predicting and classifying oxygen-binding proteins (available from http://www.imtech.res.in/raghava/oxypred/).
Oxford University Press
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