Issue 56, 2017, Issue in Progress

PepBio: predicting the bioactivity of host defense peptides

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

Supplementary files

Article information

Article type
Paper
Submitted
02 Feb 2017
Accepted
27 Jun 2017
First published
12 Jul 2017
This article is Open Access
Creative Commons BY license

RSC Adv., 2017,7, 35119-35134

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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