Determination of tDETERMINATION OF 3D STRUCTURE OF GAG POLY PROTEIN ISOLATE 90CF056 OF HIV TYPE 1 BY HIDDEN MARKOV MODEL AND NEURAL NETWhree dimensional structure of Gag Poly Protein isolate 90CF056 of HIV type 1 by Hidden Markov Model and neural networks


  • UNDETY BENJAMIN JASON Department of Bioinformatics, Sathyabama University, Chennai, Tamilnadu, India
  • Daniel Alex Anand Department of Biomedical Engineering, Sathyabama University, Chennai, Tamilnadu, India.


HMM, Gag poly-protein, Neural networks


Introduction: The study of understanding the structural and molecular conservation of HIV-1 Gag function has revealed a number of potential Gag-related targets for possible therapeutic intervention. In this study, we emphasize that our current understanding of HIV-1 Gag poly protein suggest some approaches to be as a target for novel drugs.

Objective: The functional conservation of HIV-1 Gag indicates rational drug design taking Gag as he drug target1.HIV-1 may be blocked by targeting gag poly protein. This could proffer new scheme for novel drug classes that could complement current HIV-1 treatment options.

Methods: The crystal structure of Gag poly-protein is unavailable. The templates similar are much smaller in size and thus ab-initio method is applied to determine the three dimentional structure of gag poly-protein. The value given in the program is an approximation of the probability as provided by the software with neural networks. The predictions are designed to be limited, to a score

>=.18 which is actually an approximation of the probability. The predictor is an artificial neural network. NN: Inputs indicates inclusion of separation and sequence length, e-value statistic which are based on mutual information values, a statistic based on propensity of residues in contact with each other.

Results: The local structure predictions are performed with neural networks for several different local structure alphabets, and hidden Markov models are created.

Conclusion: The complete three-dimensional model of the Gag poly protein is constructed by fold recognition and alignment to proteins in the Protein Data Bank is done.


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Guangdi Li, Jens Verheyen, Soo-Yon Rhee, Arnout Voet, Anne-Mieke Vandamme, Kristof heys:Functional conservation of HIV-1 Gag:implications. J Retrovirology 2013;10:126.

Doms RW:Beyond receptor expression:The influence of receptor conformation, density, and affinity in HIV-1 infection. J Virology 2000;276(2):229-37.

Freed EO, Martin MA, Knipe DM, Howley PM. HIVs and their replication. In:Fields Virology. Lippincott,Williams and Wilkins;Philadelphia:2007.p. 2107-85.

Melikyan GB:Common principles and intermediates of viral protein-mediated fusion:The HIV-1 paradigm. J Retrovirology 2008;5:111.

Miyauchi K, Kim Y, Latinovic O, Morozov V, Melikyan GB:HIV enters cells via endocytosis and dynamin-dependent fusion with endosomes. J Cell 2009;137(3):433-44.

Telesnitsky A, Goff SP, Coffin J, Varmus H, Hughes S. Reverse transcriptase and the generation of retroviral DNA. In:Retroviruses. Cold Spring Harbor Laboratory, Cold Spring Harbor;New York:1997.p.121-60.

Levin JG, Guo J, Rouzina I, Musier-Forsyth K:Nucleic acid chaperone activity of HIV-1 nucleocapsid protein:Critical role in reverse transcription and molecular mechanism. J Prog Nucleic Acid Res Mol Biol 2005;80:217-86.

Hulme AE, Perez O, Hope TJ:Complementary assays reveal a relationship between HIV-1 uncoating and reverse transcription. J Proc Natl Acad Sci USA 2011;108(24):9975-80.

Song B. TRIM5alpha. J Curr Top Microbiol Immunol 2009;339:47–66.

Towers GJ. The control of viral infection by tripartite motif proteins and cyclophilin A. j Retrovirology 2007;4:40.

Dismuke DJ, Aiken C:Evidence for a functional link between uncoating of the human immunodeficiency virus type 1 core and nuclear import of the viral preintegration complex. J Virol 2006;80(8):3712-20.

Yamashita M, Emerman M:Capsid is a dominant determinant of retrovirus infectivity in nondividing cells. J Virol 2004;78(11):5670-78.

Brown PO, Coffin J, Varmus H, Hughes S. Integration In:Retroviruses Cold Spring Harbor Laboratory, Cold Spring Harbor:New York;1997.p.161–205.

J Chiu HC, Wang FD, Chen YM, Wang CT, National M. Virol. Jul;87(Pt 7):.Effects of human immunodeficiency virus type 1 transframe protein p6* mutations on viral protease-mediated Gag processing. J SourceInstitute of Clinical University Taipei Taiwan 2006:2041-6.

Briggsa JD, Richesa B, Glassb V, Bartonovab G. Structure and assembly of immature HIV J. J A G Zanettiac and HG Krusslichb Author Affiliations 1.

J Huang M, Orenstein JM, Martin MA, Freed EO, Diseases NIH, et al. Nov;:.p6Gag is required for particle production from full-length human immunodeficiency virus type 1 molecular clones expressing protease. J SourceLaboratory of Molecular of Allergy and Infectious 20460 USA 2089;69(11):6810-8.

Dettenhofer M, Yu XF, Johns I, Maryland USA. Proline residues in human immunodeficiency virus type 1 p6(Gag) exert a cell type-dependent effect on viral replication and virion incorporation of Pol proteins. J Source Department of Molecular Microbiology and University School of Hygiene and Public Health Baltimore;21205.

Lovell IW, Davis WB, Arendall, III, de Bakker JM, Word MG, Prisant JS. SC PIW Richardon and D. C Richardson Structure validation by Calpha geometry phipsi and Cbeta deviation. J Proteins Structure Function Genetics 2002;50:437-50.



How to Cite

JASON, U. B., and D. A. Anand. “Determination of TDETERMINATION OF 3D STRUCTURE OF GAG POLY PROTEIN ISOLATE 90CF056 OF HIV TYPE 1 BY HIDDEN MARKOV MODEL AND NEURAL NETWhree Dimensional Structure of Gag Poly Protein Isolate 90CF056 of HIV Type 1 by Hidden Markov Model and Neural Networks”. International Journal of Pharmacy and Pharmaceutical Sciences, vol. 6, no. 8, Aug. 2014, pp. 471-3,



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