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PepBio: Predicting the bioactivity of host defense peptides
Author(s)
Simeon, Saw
Li, Hao
Win, Thet Su
Malik, Aijaz Ahmad
Kandhro, Abdul Hafeez
Piacham, Theeraphon
Shoombuatong, Watshara
Nuchnoi, Pornlada
Wikberg, Jarl E.S.
Gleeson, M. Paul
Nantasenamat, Chanin
Date Issued
January 1, 2017
Type
Article
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/.
Citation
Rsc Advances, 7(56), 35119-35134, 2017