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Structure Prediction and Active Site Analysis of New H1N1 Neuraminidase:Target for Antiviral Drug Design

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1TitleTitle of DocumentStructure Prediction and Active Site Analysis of New H1N1 Neuraminidase:Target for Antiviral Drug Design
2CreatorAuthor's name, affiliation, country VIVEK CHANDRAMOHAN*, MANJUNATH DAMMALLI, MAHANTESH BIRADAR, RICHARD L JAYARAJ, PARESH NATH KUNDU and B. S. GOWRISHANKAR
Department of Biotechnology, Siddaganga Institute of Technology, Tumkur- 572103, Karnataka, India
Department of Biotechnology, Periyar University, Salem, Tamilnadu, India
3SubjectDicipline(s) Chemical Science
3SubjectKeywords H1N1, Homology modeling, Active site, Neuraminidase
4DescriptionAbstract The H1N1 viral envelope protein neuraminidase encoded by NA gene plays a key role in the pathogenesis of swine flu. The active site of the neuraminidase protein is targeted by presently available antiviral drugs. The influenza virus often proves to be resistant to currently available drugs, due single amino acid substitutions conferred by the mutations in the gene coding for neuraminidase protein. The latest Influenza A virus A/Perth/262/2009(H1N1) sequence with accession number ADJ67981 was selected from NCBI. The BLAST program was used to identify the best template structure, which was found to be 3NSS_A. Sequence alignment was carried out with the template and query sequence, the identity and similarity was found to be 81.9% and 82.6% respectively. Homology modeling was performed using Accelrys Discovery Studio 3.5 software, the model with the lowest energy was then assessed for stereochemical quality and side-chain environment. The PDF energy and DOPE score of the best modeled structure was 2090.1682 and -43752.3632 respectively. Further active site optimization of the modeled protein was performed by molecular dynamics. The key active site residues which are crucial for further docking studies were ascertained.
5PublishersOrganizing agency, location WWW Publications, India
6Contributor Sponsor(s) -
7DateDate (YYYY-MM-DD) -
8TypeStatus & genre Peer-reviewed Article
8TypeType
9FormateFile Formate PDF
10IdentifierUniform Resource Identifier Click Here
10IdentifierDigital Object Identifier DOI:10.7598/cst2014.715
11SourceJournal/conference title; vol., no. (Year)Chemical Science Transactions, Volume  3 , Number  (4), (2014)
12LanuguageEnglish=en en
13RelationSupp.files
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Chemical Science Transactions | Chem Sci Trans | CST | Online Chemistry Journal | Open Access
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