title: Prediction of β-lactamase and its class by Chou's pseudo-amino acid composition and support vector machine.
abstract: β-Lactam class of antibiotics is used as major therapeutic agent against a number of pathogenic microbes. The widespread and indiscriminate use of antibiotics to treat bacterial infection has prompted evolution of several evading mechanisms from the lethal effect of antibiotics. β-Lactamases are endogenously produced enzyme that makes bacteria resistant against β-lactam antibiotics by cleaving the β-lactam ring. On the basis of primary structures, β-lactamase family of enzymes is divided into four classes namely A, B, C and D. Class B are metallo-enzymes while A, C and D does not need any metal in the enzyme catalysis. In the present study we developed a SVM based two level β-lactamases protein prediction method, which differentiate β-lactamases from non-β-lactamases at first level and then classify predicted β-lactamases into different classes at second level. We evaluated performance of different input vectors namely simple amino acid composition, Type-1 and Type-2 Chou's pseudo amino acid compositions. Comparative performances indicated that SVM model trained on Type-1 pseudo amino acid composition has the best performance. At first level we were able to classify β-lactamases from non-β-lactamases with 90.63% accuracy. At second level we found maximum accuracy of 61.82%, 89.09%, 70.91% and 70.91% of class A, class B, class C and class D, respectively. A web-server as well as standalone, PredLactamase, is also developed to make the method available to the scientific community, which can be accessed at http://14.139.227.92/mkumar/predlactamase.
authors.affiliation: Department of Biophysics, University of Delhi South Campus, New Delhi, India.
authors.forename: Ravindra
authors.initials: R
authors.lastname: Kumar
authors.affiliation: Department of Biophysics, University of Delhi South Campus, New Delhi, India.
authors.forename: Abhishikha
authors.initials: A
authors.lastname: Srivastava
authors.affiliation: Department of Biophysics, University of Delhi South Campus, New Delhi, India.
authors.forename: Bandana
authors.initials: B
authors.lastname: Kumari
authors.affiliation: Department of Biophysics, University of Delhi South Campus, New Delhi, India. Electronic address: manish@south.du.ac.in.
authors.forename: Manish
authors.initials: M
authors.lastname: Kumar
mesh_terms: D000595:Amino Acid Sequence; D000890:Anti-Infective Agents / Q000737:chemistry; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein / Q000379:methods*; D060388:Support Vector Machine; D001618:beta-Lactamases / Q000737:chemistry / Q000145:classification / Q000235:genetics; D047090:beta-Lactams / Q000737:chemistry
chemical_list: D000890:Anti-Infective Agents; D047090:beta-Lactams; D001618:beta-Lactamases
keywords: Antibiotic resistance; Leave-one-out cross-validation; β-Lactamase protein