Using reduced amino acid composition to predict defensin family and subfamily: Integrating similarity measure and structural alphabet.

Abstract:

:Defensins are essentially ancient natural antibiotics with potent activity extending from lower organisms to humans. They can inhibit the growth or virulence of micro-organisms directly or indirectly enhance the host's immune system. The successful prediction of defensin peptides will provide very useful information and insights for the basic research of defensins. In this study, by selecting the N-peptide composition of reduced amino acid alphabet (RAAA) obtained from structural alphabet named Protein Blocks as the feature parameters, the increment of diversity (ID) is firstly developed to predict defensins family and subfamily. The jackknife test based on 2-peptide composition of reduced amino acid alphabet (RAAA) with 13 reduced amino acids shows that the overall accuracy of prediction are 91.36% for defensin family, and 94.21% for defensin subfamily. The results indicate that ID_RAAA is a simple and efficient prediction method for defensin peptides.

journal_name

Peptides

journal_title

Peptides

authors

Zuo YC,Li QZ

doi

10.1016/j.peptides.2009.06.032

subject

Has Abstract

pub_date

2009-10-01 00:00:00

pages

1788-93

issue

10

eissn

0196-9781

issn

1873-5169

pii

S0196-9781(09)00273-3

journal_volume

30

pub_type

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