Refine your search
Collections
Co-Authors
Year
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z All
Singh, Gurmit
- Comparative Homology Modelling for HPV Type 16 E 7 Proteins by using MODELLER and its Validations with SAVS and ProSA Web Server
Abstract Views :625 |
PDF Views:0
Authors
Affiliations
1 Department of Computational Biology & Bioinformatics, Sam Higginbottom Institute of Agriculture, Technology & Sciences Deemed to be University, Allahabad - 211007, IN
2 Department of Computer Science & Information Technology, SHIATS, Allahabad - 211007, IN
1 Department of Computational Biology & Bioinformatics, Sam Higginbottom Institute of Agriculture, Technology & Sciences Deemed to be University, Allahabad - 211007, IN
2 Department of Computer Science & Information Technology, SHIATS, Allahabad - 211007, IN
Source
Journal of Computational Intelligence in Bioinformatics, Vol 6, No 1 (2013), Pagination: 27-33Abstract
Human papillomaviruses (HPV) are a group of viruses which are associated with various proliferative diseases in the infected epithelium. HPV types 6, 11, 16, and 18 are the most common, are associated with lesions in the anogenital tract. The "benign" types 6 and 11 are mainly associated with condylomata acuminate of the oncogenic HPV types, HPV-16 is most frequently found in cervical carcinomas. The 3-dimentional structure of the protein was not yet available in Protein Data Bank; hence the present paper of predicting the 3D model of the HPV Type 16 E7 proteins. Template based homology modelling predicts the three-dimensional structure of hpv type 16 E 7 protein sequence (target) based primarily on its alignment to one or more proteins of known structure as template generated by MODELLER. The prediction process consists of target-template alignment, model building, and model evaluation. The model was checked for stereo chemical quality by PROCHECK, VERIFY 3D, WHAT IF, ERRAT AND ProSA servers were also used for the display of Z-scores and energy plots. Finally the protein was visualized with Swiss-PDB viewer.Keywords
Homology Modelling, SAVS, ProSA Servers, Human Papilloma Virus
References
- Tremonton, A. and Morea, V. (2003) Assessment of homology-based predictions in CASP5. Proteins, 53 (Suppl. 6), 352–368.
- Pfister H. Biology and biochemistry of papillomaviruses. Rev Physiol Biochem Pharmacol 1984; 99: 112-81.
- Pfister H. Human papillomaviruses and genital cancer. Adv Cancer Res 1987; 48:113-47
- Cullen AP, Reid R, Campion M, Lorincz AT. Analysis of The physical state of different human papillomavirus DNAs in intra-epithelial an invasive cervical neoplasm. J Viro1991; 65:606-12.
- Pfister H. Human papillomaviruses and genital cancer. Adv CancerRes 1987; 48:113-47.
- Cullen AP, Reid R, Campion M, Lorincz AT. Analysis of The physical state of different human papillomaviruses DNAs in intraepithelial an invasive cervical neoplasm. J Viro1991; 65:606-12.
- Yee C, Krishnan-Hewlett I, Baker CC, Schlegel R, Howley PM. Presence and expression of human papillomaviruses sequences in human cervical carcinoma cell lines. Am Pathol 1985; 119:361-6.
- Van den Brule AJ, Cromme FV, Snijders PJ, Smit L, Oudejans CB, Baak JP, et al. Nonradioactive RNA in situ hybridization detection of human papillomaviruses 16-E7.
- N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modelling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.
- M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sanchez, F. Melo, A. Sali. Comparative protein structure modelling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.
- A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.
- A. Fiser, R.K. Do & A. Sali. Modelling of loops in protein structures, Protein Science 9. 1753-1773, 2000.
- Laskowski R A, MacArthur M W, Moss D S and Thornton J M (1993). PROCHECK: a program to check the stereo chemical quality of protein structures. J. Appl. Cryst., 26, 283-291.
- WHAT IF: a molecular modelling and drug design program, G.Vriend, J. Mol. Graph. 8, 52—56 (1990).
- WHAT_CHECK (verification routines from WHAT IF) R.W.W.Hooft, G.Vriend, C.Sander and E.E. Abola, Errors in protein structures .Nature 381, 272 (1996).
- Ramachandran plot: G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan, Stereochemistry of Polypeptide Chain Conformations. J. Mol. Biol. 7, 95--99 (1963).
- Sippl, M.J. (1993), Recognition of Errors in Three-Dimensional Structures of Proteins. Proteins 17, 355-362.
- Colovos C & Yeates TO, Protein Sci. 1993 2: 1511 [PMID: 8401235]
- VERIFY3D: assessment of protein models with three-dimensional profiles: Eisenberg D, Lüthy R, Bowie JU.Source Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles 90095, USA. [PMID: 9379925].
- Pontius J, Richelle J, Wodak SJ. (1996). Deviations from standard atomic volumes as a quality measure for protein crystal structures. J. Mol. Biol. 264, 121-136.
- Wildenstein & Sippl (2007), ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research 35, W407-W410.
- Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11; 22(22):4673-80.