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PepBio: predicting the bioactivity of host defense peptides
Mahidol Univ, Ctr Data Min & Biomed Informat, Fac Med Technol, Bangkok 10700, Thailand.;Kasetsart Univ, Fac Sci, Interdisciplinary Grad Program Biosci, Bangkok 10900, Thailand..
Mahidol Univ, Ctr Data Min & Biomed Informat, Fac Med Technol, Bangkok 10700, Thailand..
Mahidol Univ, Ctr Data Min & Biomed Informat, Fac Med Technol, Bangkok 10700, Thailand..
Mahidol Univ, Ctr Data Min & Biomed Informat, Fac Med Technol, Bangkok 10700, Thailand..
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2017 (English)In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, no 56, 35119-35134 p.Article in journal (Refereed) Published
Abstract [en]

Host defense peptides (HDPs) represents a class of ubiquitous and rapid responding immune molecules capable of direct inactivation of a wide range of pathogens. Recent research has shown HDPs to be promising candidates for development as a novel class of broad-spectrum chemotherapeutic agent that is effective against both pathogenic microbes and malignant neoplasm. This study aims to quantitatively explore the relationship between easy-to-interpret amino acid composition descriptors of HDPs with their respective bioactivities. Classification models were constructed using the C4.5 decision tree and random forest classifiers. Good predictive performance was achieved as deduced from the accuracy, sensitivity and specificity in excess of 90% and Matthews correlation coefficient in excess of 0.5 for all three evaluated data subsets (e.g. training, 10-fold cross-validation and external validation sets). The source code and data set used for the construction of classification models are available on GitHub at https://github.com/chaninn/pepbio/.

Place, publisher, year, edition, pages
2017. Vol. 7, no 56, 35119-35134 p.
National Category
Pharmaceutical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-331956DOI: 10.1039/c7ra01388dISI: 000405811400023OAI: oai:DiVA.org:uu-331956DiVA: diva2:1151053
Funder
Swedish Research Council, E09/2557
Available from: 2017-10-20 Created: 2017-10-20 Last updated: 2017-10-20Bibliographically approved

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Wikberg, Jarl E. S.

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