A Cumulative Strategy to Predict and Characterize Antimicrobial Peptides (AMPs) from Protein Database Gayathri Ravichandran 1,2 • Venkatesh Kumaresan 1 • Prasanth Bhatt 1 • Mariadhas Valan Arasu 3 • Naif Abdullah Al-Dhabi 3 • Jesu Arockiaraj 1 Accepted: 6 October 2016 Ó Springer Science+Business Media New York 2016 Abstract Antimicrobial peptides (AMPs) are indivisible part of the innate immune system in invertebrates. AMPs have been proven to have crucial role with a wide range of biological activities, mainly with immunomodulatory and broad spectrum of antimicrobial activity against various pathogens. The unique and salient features of the AMPs show its exceptional nature of therapeutic activity and serves as an alternative agent for conventional antibiotics. The search for potential AMPs persist, as the emergence of multiple drug resistant bacterial strains has been spreading in higher number. Here, the putative antimicrobial peptide sequences were identified from 19,915 sequences of prawn transcriptome and analyzed with various in silico tools such as EXPASY, AMPA, and helical wheel projection and so on. The characteristic antimicrobial properties have been determined for 660 putative AMPs with above men- tioned tools. We have demonstrated an efficient bioinfor- matics approach to derive and analyze the AMPs from the transcriptome data of Macrobrachium rosenbergii. Even though, 660 peptide regions were identified among those five peptide sequences were demonstrated comprehen- sively with each characteristic property contributes the antimicrobial activity. In this study, we have proposed a rapid and successful protocol that would help to predict AMP in sequential procedure using various in silico methods. Also, we have shown a distinctive method to shortlist the AMPs based on their various physico-chemical properties. Until now, no sequential protocol has been developed to identify and characterize the AMPs from protein database. Keywords Antimicrobial peptide Á Transcriptome Á Protein database Á Prawn Introduction The biological system follows a collection of immune responses to defend them against the pathogenic microbial environment. The immune response varied among the invertebrates, plants, vertebrates, and even from one spe- cies to another. Unlike vertebrates, the innate immunity holds the major host response against the pathogenic infection in plants and invertebrates. Among the innate immune components, the antimicrobial peptides (AMPs) play a crucial role in protecting the organisms from various microbial attacks (Radek and Gallo 2007). In addition to the complex structure, the peptides kill the bacteria by affecting the multiple targets which impede the bacteria to develop resistance (Park et al. 2011). Up to date, over 5000 AMPs have been reported and some of those are in various levels of clinical and preclinical studies (Bahar and Ren 2013). The identified AMPs are categorized based on their difference in secondary structures, composition and arrangement of amino acids, which contributes majorly for its bactericidal property (Schmidt and Wong 2013). Recently, there has been an extensive development in the investigations of AMPs. The discovery of magainin, an AMP & Jesu Arockiaraj jesuaraj@hotmail.com 1 Division of Fisheries Biotechnology & Molecular Biology, Department of Biotechnology, Faculty of Science and Humanities, SRM University, Kattankulathur, Chennai, Tamil Nadu 603 203, India 2 SRM Research Institute, SRM University, Kattankulathur, Chennai, Tamil Nadu 603 203, India 3 Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia 123 Int J Pept Res Ther DOI 10.1007/s10989-016-9559-z