Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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hpvPDB: An Online Proteome Reserve for Human Papillomavirus

  • Kumar, Satish (Bioinformatics Centre and Biochemistry, Mahatma Gandhi Institute of Medical Sciences) ;
  • Jena, Lingaraja (Bioinformatics Centre and Biochemistry, Mahatma Gandhi Institute of Medical Sciences) ;
  • Daf, Sangeeta (Datta Meghe Institute of Medical Sciences (Deemed University)) ;
  • Mohod, Kanchan (Bioinformatics Centre and Biochemistry, Mahatma Gandhi Institute of Medical Sciences) ;
  • Goyal, Peyush (Department of Biotechnology, Ministry of Science and Technology) ;
  • Varma, Ashok K. (Advanced Centre for Treatment, Research and Education in Cancer)
  • Received : 2013.09.23
  • Accepted : 2013.11.19
  • Published : 2013.12.31
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Abstract

Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The molecular understanding of HPV proteins has significant connotation for understanding their intrusion in the host and designing novel protein vaccines and anti-viral agents, etc. Genomic, proteomic, structural, and disease-related information on HPV is available on the web; yet, with trivial annotations and more so, it is not well customized for data analysis, host-pathogen interaction, strain-disease association, drug designing, and sequence analysis, etc. We attempted to design an online reserve with comprehensive information on HPV for the end users desiring the same. The Human Papillomavirus Proteome Database (hpvPDB) domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Simultaneous easy expandability and retrieval of the strain-specific data, with a provision for sequence analysis and exploration potential of predicted structures, and easy access for curation and annotation through a range of search options at one platform are a few of its important features. Affluent information in this reserve could be of help for researchers involved in structural virology, cancer research, drug discovery, and vaccine design.

Keywords

References

  1. Tungteakkhun SS, Filippova M, Neidigh JW, Fodor N, Duerksen-Hughes PJ. The interaction between human papillomavirus type 16 and FADD is mediated by a novel E6 binding domain. J Virol 2008;82:9600-9614. https://doi.org/10.1128/JVI.00538-08
  2. Watts KJ, Thompson CH, Cossart YE, Rose BR. Variable oncogene promoter activity of human papillomavirus type 16 cervical cancer isolates from Australia. J Clin Microbiol 2001;39: 2009-2014. https://doi.org/10.1128/JCM.39.5.2009-2014.2001
  3. Zheng ZM, Baker CC. Papillomavirus genome structure, expression, and post-transcriptional regulation. Front Biosci 2006;11:2286-2302. https://doi.org/10.2741/1971
  4. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, et al. The Proteomics Protocols Handbook. Totowa: Humana Press, 2005. pp. 571-607.
  5. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, et al. Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci 2007; Chapter 2:Unit 2.9.
  6. Arnold K, Bordoli L, Kopp J, Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 2006;22:195-201. https://doi.org/10.1093/bioinformatics/bti770
  7. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-291. https://doi.org/10.1107/S0021889892009944
  8. Wiederstein M, Sippl MJ. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 2007;35:W407-W410. https://doi.org/10.1093/nar/gkm290
  9. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
  10. Jmol: an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. Jmol. Accessed 2013 Feb 5. Available from: http://www.jmol.org/.
  11. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 2008;36:W465-W469. https://doi.org/10.1093/nar/gkn180
  12. Myers G, Baker C, Wheeler C, Halpern A, McBride A, Doorbar J. Human papillomaviruses: a compilation and analysis of nucleic acid and amino acid sequences. Los Alamos: Theoretical Biology and Biophysics, Los Alamos National Laboratory, 1994-1997. Accessed 2013 Nov 10. Available from: http:// pave.niaid.nih.gov/lanl-archives/HPVcompintro4. html.

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