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Online Journal of Bioinformatics©
Volume 20(3): 272-290, 2019.
Computational Prediction of 3D Structure for the Matrix Protein2 (BM2) of Influenza B Virus.
Anshul Tiwari1, Ashish Chandra Trivedi1, Aditya Narain Sarangi2, Prachi Srivastava1*
1Amity Institute of Biotechnology, Lucknow India, 2BMIC, SGPGIMS, Lucknow India
Tiwari A, Trivedi AC, Sarangi AN, Srivastava P., Computational Prediction of 3D Structure for the Matrix Protein2 (BM2) of Influenza B Virus, Onl J Bioinform., 20(3): 272-290, 2019. We modelled BM2 protein of Influenza B virus (isolate B/Lee/1940) using PDBSUM, using 20 proteins with sequence similarities to BM2 and available structural data templates. Templates were then exported to Discovery Studio 2.0 with a cluster of 4 proteins with alpha-helices and beta-sheets. Because of limited similarities with BM2 sequence an iterative error and trial modeling procedure for structure validation and energy refinement was undertaken with MODELLER, DOPE, PROCHECK, PROSA, WHATIF and CHARMM. The resulting model consisted of 4 alpha helices and 2 anti-parallel beta sheets with good overall stereochemistry and 90% residue psi/phi angles falling in the most favored regions. The model may be useful for design of a BM2 inhibitor to treat flu.
Key Words: Influenza B matrix2 protein, Viral Ribonucleic Acid, Homology Modeling.