SVM Prediction of Ligand-binding Sites in Bacterial Lipoproteins Employing Shape and Physio-chemical Descriptors
2012
Bacterial lipoproteins play critical roles in various physiological processes including the maintenance of pathogenicity
and numbers of them are being considered as potential candidates for generating novel vaccines. In this work, we
put forth an algorithm to identify and predict ligand-binding sites in bacterial lipoproteins. The method uses three types of
pocket descriptors, namely fpocket descriptors, 3D Zernike descriptors and shell descriptors, and combines them with Support
Vector Machine (SVM) method for the classification. The three types of descriptors represent shape-based properties
of the pocket as well as its local physio-chemical features. All three types of descriptors, along with their hybrid combinations
are evaluated with SVM and to improve classification performance, WEKA-InfoGain feature selection is applied. Results
obtained in the study show that the classifier successfully differentiates between ligand-binding and non-binding pockets.
For the combination of three types of descriptors, 10 fold cross-validation accuracy of 86.83% is obtained for training
while the selected model achieved test Matthews Correlation Coefficient (MCC) of 0.534. Individually or in combination
with new and existing methods, our model can be a very useful tool for the prediction of potential ligand-binding sites in
bacterial lipoproteins.
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