title: Predicting antimicrobial peptides with improved accuracy by incorporating the compositional, physico-chemical and structural features into Chou's general PseAAC.
abstract: Antimicrobial peptides (AMPs) are important components of the innate immune system that have been found to be effective against disease causing pathogens. Identification of AMPs through wet-lab experiment is expensive. Therefore, development of efficient computational tool is essential to identify the best candidate AMP prior to the in vitro experimentation. In this study, we made an attempt to develop a support vector machine (SVM) based computational approach for prediction of AMPs with improved accuracy. Initially, compositional, physico-chemical and structural features of the peptides were generated that were subsequently used as input in SVM for prediction of AMPs. The proposed approach achieved higher accuracy than several existing approaches, while compared using benchmark dataset. Based on the proposed approach, an online prediction server iAMPpred has also been developed to help the scientific community in predicting AMPs, which is freely accessible at http://cabgrid.res.in:8080/amppred/. The proposed approach is believed to supplement the tools and techniques that have been developed in the past for prediction of AMPs.
authors.affiliation: Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi-110012, India.
authors.forename: Prabina Kumar
authors.initials: PK
authors.lastname: Meher
authors.affiliation: Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi-110012, India.
authors.forename: Tanmaya Kumar
authors.initials: TK
authors.lastname: Sahu
authors.affiliation: Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi-110012, India.|Department of Bioinformatics, Janta Vedic College, Baraut, Baghpat-250611, Uttar Pradesh, India.
authors.forename: Varsha
authors.initials: V
authors.lastname: Saini
authors.affiliation: Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi-110012, India.
authors.forename: Atmakuri Ramakrishna
authors.initials: AR
authors.lastname: Rao
mesh_terms: D000935:Antifungal Agents / Q000737:chemistry; D023181:Antimicrobial Cationic Peptides / Q000737:chemistry*; D000998:Antiviral Agents / Q000737:chemistry; D019540:Area Under Curve; D055598:Chemical Phenomena; D030562:Databases, Protein; D012372:ROC Curve; D060388:Support Vector Machine
chemical_list: D000935:Antifungal Agents; D023181:Antimicrobial Cationic Peptides; D000998:Antiviral Agents