Abstract—The MMPs and ADAMs are cell surface proteases which belong to metalloprotease family. They play an important role in skin aging, skin disorders, anticancer therapy and other physiological disorders. Thus there arises the need to understand the relationships among various parameters of these proteins for prediction of their classes, structures and functionality. The computational approaches for prediction of their classes are fast and economical therefore can be used to complement the existing wet lab techniques. Realizing their importance, in this paper an attempt has been made to correlate them with their amino acid composition and predict them with fair accuracy. This is a novel method where ADAMs and MMPs have been classified on the basis of amino acid composition using Support Vector Machine. The SVM has been implemented using Lib SVM package. The method discriminates MMP subfamily from ADAM proteases with Matthew's correlation coefficient of 0.98 using amino acid composition. The method is further able to predict three major subclasses or subfamilies of MMPs with an overall Matthew's correlation coefficient [MCC] and accuracy of 0.782 and 89.01% respectively using amino acid composition. The performance of the method was evaluated using 5-fold cross-validation where accuracy of 98% was obtained.
Index Terms—Metalloproteinases; Support vector machine; Amino Acid composition; Kernel functions.
K. Pant is with Bioinformatics Department, MANIT, Bhopal, India [e-mail: firstname.lastname@example.org].N. Adlakha is with Applied Mathematics Department, SVNIT, Surat, India [e-mail: email@example.com].
A. Mittal is with Department of Chemistry, MANIT, Bhopal, India [email:firstname.lastname@example.org].
Cite: Kumud pant, Neeru Adlakha and Alok Mittal, "Multi Class Classification Approach for Classification of ADAMs, MMPs and Their Subclasses," International Journal of Engineering and Technology vol. 2, no. 3, pp. 302-307, 2010.