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Title
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Functional assignment to JEV proteins using SVM
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Authors
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Ganesh Chandra Sahoo1,*, Manas Ranjan Dikhit1 and Pradeep Das1
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Affiliation
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1BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna-800007, India
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ganeshiitkgp@gmail.com; * Corresponding author
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Article Type
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Hypothesis
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Date
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received May 24, 2008; revised July 08, 2008; accepted July 20, 2008; published September 02, 2008
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Abstract |
Identification of different protein functions facilitates a mechanistic understanding of Japanese encephalitis virus (JEV) infection and opens novel means for drug development. Support vector machines (SVM), useful for predicting the functional class of distantly related proteins, is employed to ascribe a possible functional class to Japanese encephalitis virus protein. Our study from SVMProt and available JE virus sequences suggests that structural and nonstructural proteins of JEV genome possibly belong to diverse protein functions, are expected to occur in the life cycle of JE virus. Protein functions common to both structural and non-structural proteins are iron-binding, metal-binding, lipid-binding, copper-binding, transmembrane, outer membrane, channels/Pores - Pore-forming toxins (proteins and peptides) group of proteins. Non-structural proteins perform functions like actin binding, zinc-binding, calcium-binding, hydrolases, Carbon-Oxygen Lyases, P-type ATPase, proteins belonging to major facilitator family (MFS), secreting main terminal branch (MTB) family, phosphotransfer-driven group translocators and ATP-binding cassette (ABC) family group of proteins. Whereas structural proteins besides belonging to same structural group of proteins (capsid, structural, envelope), they also perform functions like nuclear receptor, antibiotic resistance, RNA-binding, DNA-binding, magnesium-binding, isomerase(intramolecular), oxidoreductase and participate in type II (general) secretory pathway (IISP).
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Keywords
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Japanese encephalitis virus (JEV); protein function family; support vector machine; SVMProt
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Citation
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Sahoo et al., Bioinformation 3(1): 1-7 (2008)
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Edited by
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P. Kangueane
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ISSN
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0973-2063
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Publisher
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Biomedical Informatics
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License
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This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.
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