Available online at www.scholarsresearchlibrary.com Scholars Research Library Annals of Biological Research, 2010, 1 (2) : 16-22 (http://scholarsresearchlibrary.com/archive.html) ISSN 0976-1233 16 Scholars Research Library In silico epitope structure prediction for matrix protein of H1N1 AnupTripathi, Deepesh Kumar, Sachidanand Singh, Atul Kumar, Manitha T. P., Babu Ram, K. Panneerselvam and J. Jannet Vennila Department of Bioinformatics, School of Biotechnology and Health Sciences, Karunya University, Coimbatore, Tamil Nadu, India ______________________________________________________________________________ Abstract H1N1is a current endemic in both human and pig populations and is the cause of Swine flu in humans. Bioinformatics tools enable us to move rapidly from protein sequence to vaccine design. ProPred-I, Rankpep and PeptGen are servers used for identification of epitope with the help of artificial neural network approach. For H1N1 we identified 10 matrix proteins (M1) which are mainly responsible for propagation of H1N1. From ProPred-I,Rankpep and PeptGen conserved 40 epitopes were identified by their selective algorithms and scoring matrices. A virtual library was designed for the 40 epitopes and further it was used for epitope conservancy analysis tool (IEDB) to narrow down the list of putative epitopes to 20 only. A structural library of all conserved putative epitopes was then minimized with Prime Schrodinger module and then ten putative epitopes were designedwith the motto of identifying best virtual vaccine. The pace of vaccine design will accelerate when these in silico results combined with in vitro methods for screening and confirming epitope. Key words: Capsid Protein, peptide, epitope, matrix protein, H1N1. _____________________________________________________________________________ INTRODUCTION A serotype of Influenza virus A, H1N1 is a current endemic in both human and pig populations and is the cause of Swine flu in humans [1]. Influenza ‘A’ viruses are enveloped RNA viruses with an eight-segmented, single-stranded, negative-sense genome belonging to the family Orthomyxoviridae. The segment of influenza A virus having eight gene, encoded 10 proteins: hemagglutinin (HA), neuraminidase (NA), matrix proteins M2 and M1, nonstructural (NS) proteins NS1 and NS2, the nucleocapsid, and the three polymerases, the PB1 (polymerase basic 1), PB2, and PA (polymerase acidic) proteins [2].Influenza type A viruses are sub-typed based upon the HA and NA antigens, which are surface proteins found on the viral envelope [3]. The capsid is the protein shell of a virus encloses the genetic material of the virus. Matrix protein of H1N1 virus is the outer covering which contains the epitope detection site [4]. So by designing