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Online Journal of Bioinformatics ©
Volume 20(2):89-111, 2019.
Computational prediction of 3D structure for matrix protein2 (BM2) influenza B virus.
Anshul Tiwari1, Ashish Chandra Trivedi1, Aditya Narain Sarangi2, Prachi Srivastava1*
1 Amity 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 Bioinfo., 20(2):89-111, 2019. We report a model for BM2 protein of the Influenza B virus (isolate B/Lee/1940) by PDBSUM, 20 proteins with sequence similarities with BM2 protein and available structural data used as templates. These were imported in to Discovery Studio 2.0, and two separate clusters were identified; one with 4 proteins that had both alpha-helices and beta-sheets were selected as templates. Because of the limited similarities of these templates with the BM2 sequence, an iterative error and trial modeling procedure was undertaken using the comparative modeling program MODELLER, structure validation programs (namely DOPE, PROCHECK, PROSA and WHATIF) and energy refinement using the program CHARMM. The resulting model consisted of four alpha helices and two anti parallel beta sheets and has a good overall stereochemistry with 90% of the residue psi/phi angles falling in the most favored regions. The model may provide a valuable aid in design for inhibition of BM2 induced flu.
Key Words: Influenza B matrix2 protein, Viral Ribonucleic Acid, Homology Modeling.