{"title":"Physico-chemical features for recognition of antimicrobial peptides","authors":"Daniel Veltri, Amarda Shehu","doi":"10.1109/BIBMW.2012.6470274","DOIUrl":null,"url":null,"abstract":"Concerns over antibacterial resistance have antimicrobial peptides (AMPs) garnering attention as potential targets for new antibacterial drugs [1]. Wet-lab development of AMP-based drugs hinge on understanding the relationship between AMP sequence and activity [1]. In support of such efforts, we devise a method to highlight position-based physico-chemical features related to activity. We do so in a focused analysis of the mature peptide fragments of cathelicidins; a populous sequence-diverse family of well-studied a-helical AMPs [1]. We employ features based on the AAIndex [2], an extensive collection of documented physico-chemical amino acid properties, and Support Vector Machine (SVM) to recognize cathelicidins from a set of carefully designed decoy sequences. Our results demonstrate that these features are very useful in elucidating specific residue positions and properties related to AMP activity.","PeriodicalId":6392,"journal":{"name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2012-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/BIBMW.2012.6470274","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 1
Abstract
Concerns over antibacterial resistance have antimicrobial peptides (AMPs) garnering attention as potential targets for new antibacterial drugs [1]. Wet-lab development of AMP-based drugs hinge on understanding the relationship between AMP sequence and activity [1]. In support of such efforts, we devise a method to highlight position-based physico-chemical features related to activity. We do so in a focused analysis of the mature peptide fragments of cathelicidins; a populous sequence-diverse family of well-studied a-helical AMPs [1]. We employ features based on the AAIndex [2], an extensive collection of documented physico-chemical amino acid properties, and Support Vector Machine (SVM) to recognize cathelicidins from a set of carefully designed decoy sequences. Our results demonstrate that these features are very useful in elucidating specific residue positions and properties related to AMP activity.