NDLI: Using increment of diversity to predict mitochondrial proteins of malaria parasite: integrating pseudo-amino acid composition and structural alphabet

Content Provider	Springer Nature Link
Author	Chen, Ying Li Li, Qian Zhong Zhang, Li Qing
Copyright Year	2010
Abstract	Due to the complexity of Plasmodium falciparum (PF) genome, predicting mitochondrial proteins of PF is more difficult than other species. In this study, using the n-peptide composition of reduced amino acid alphabet (RAAA) obtained from structural alphabet named Protein Blocks as feature parameter, the increment of diversity (ID) is firstly developed to predict mitochondrial proteins. By choosing the 1-peptide compositions on the N-terminal regions with 20 residues as the only input vector, the prediction performance achieves 86.86% accuracy with 0.69 Mathew’s correlation coefficient (MCC) by the jackknife test. Moreover, by combining with the hydropathy distribution along protein sequence and several reduced amino acid alphabets, we achieved maximum MCC 0.82 with accuracy 92% in the jackknife test by using the developed ID model. When evaluating on an independent dataset our method performs better than existing methods. The results indicate that the ID is a simple and efficient prediction method for mitochondrial proteins of malaria parasite.
Starting Page	1309
Ending Page	1316
Page Count	8
File Format	PDF
ISSN	09394451
Journal	Amino Acids
Volume Number	42
Issue Number	4
e-ISSN	14382199
Language	English
Publisher	Springer Vienna
Publisher Date	2010-12-30
Publisher Place	Vienna
Access Restriction	Subscribed
Subject Keyword	Plasmodium falciparum Mitochondrial proteins Increment of diversity Reduced amino acid alphabet Hydropathy distribution Neurobiology Proteomics Biochemical Engineering Life Sciences Biochemistry Analytical Chemistry
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Biochemistry Clinical Biochemistry

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