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Issue 56, 2017, Issue in Progress
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PepBio: predicting the bioactivity of host defense peptides

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Abstract

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/.

Graphical abstract: PepBio: predicting the bioactivity of host defense peptides

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Publication details

The article was received on 02 Feb 2017, accepted on 27 Jun 2017 and first published on 12 Jul 2017


Article type: Paper
DOI: 10.1039/C7RA01388D
Citation: RSC Adv., 2017,7, 35119-35134
  • Open access: Creative Commons BY license
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    PepBio: predicting the bioactivity of host defense peptides

    S. Simeon, H. Li, T. S. Win, A. A. Malik, A. H. Kandhro, T. Piacham, W. Shoombuatong, P. Nuchnoi, J. E. S. Wikberg, M. P. Gleeson and C. Nantasenamat, RSC Adv., 2017, 7, 35119
    DOI: 10.1039/C7RA01388D

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      [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the Centre National de la Recherche Scientifique (CNRS) and the RSC.
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      [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the European Society for Photobiology, the European Photochemistry Association, and RSC.
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      [Original citation] - Published by The Royal Society of Chemistry.

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