title: Leveraging family-specific signatures for AMP discovery and high-throughput annotation.
abstract: Antimicrobial peptides (AMPs) are diverse, biologically active, essential components of the innate immune system. As compared to conventional antibiotics, AMPs exhibit broad spectrum antimicrobial activity, reduced toxicity and reduced microbial resistance. They are widely researched for their therapeutic potential, especially against multi-drug resistant pathogens. AMPs are known to have family-specific sequence composition, which can be mined for their discovery and rational design. Here, we present a detailed family-based study on AMP families. The study involved the use of sequence signatures represented by patterns and hidden Markov models (HMMs) present in experimentally studied AMPs to identify novel AMPs. Along with AMPs, peptides hitherto lacking antimicrobial annotation were also retrieved and wet-lab studies on randomly selected sequences proved their antimicrobial activity against Escherichia coli. CAMPSign, a webserver has been created for researchers to effortlessly exploit the use of AMP family signatures for identification of AMPs. The webserver is available online at www.campsign.bicnirrh.res.in. In this work, we demonstrate an optimised and experimentally validated protocol along with a freely available webserver that uses family-based sequence signatures for accelerated discovery of novel AMPs.
authors.affiliation: Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai-400012, India.
authors.forename: Faiza Hanif
authors.initials: FH
authors.lastname: Waghu
authors.affiliation: Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai-400012, India.
authors.forename: Ram Shankar
authors.initials: RS
authors.lastname: Barai
authors.affiliation: Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai-400012, India.
authors.forename: Susan
authors.initials: S
authors.lastname: Idicula-Thomas
mesh_terms: D000595:Amino Acid Sequence; D023181:Antimicrobial Cationic Peptides / Q000737:chemistry*; D057166:High-Throughput Screening Assays; D017386:Sequence Homology, Amino Acid
chemical_list: D023181:Antimicrobial Cationic Peptides