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Online Journal of Bioinformatics ©
Volume 12(2):304-313, 2011.
Molecular docking ribavirin with RNA-dependent RNA polymerase crimean-congo hemorrhagic fever virus.
Sitansu Kumar Verma*, Shivam Pratap Singh Yadav, Rhishika Singh, Ajay Kumar
Department of Biotechnology, Institute of Biomedical Education and Research, Mangalayatan University, Aligarh, India.
Kumar Verma S, Singh Yadav SP, Singh R, Kumar A, Molecular docking ribavirin with RNA-dependent RNA polymerase crimean-congo hemorrhagic fever virus, Onl J Bioinform., 12(2):304-313, 2011. Crimean-Congo hemorrhagic fever is a widespread tick borne viral disease affecting animals and humans. The viral membrane has RNA-dependent RNA polymerase (RDRP) which catalyses RNA synthesis in target cells. Inhibiting RDRP may thus prevent virus replication in host cells. The amino acid sequence of RDRP (Accession No: ACM78472.1) CCHF virus was retrieved from NCBI and a 3D model was built with Modeller9v8. The templates for RDRP protein were downloaded from PDB ID:3PHU. Homologous templates of RDRP exhibited sequence identity of 93.44% with the target. The RDRP model was then optimized with Modeller, validated through PROCHECK and submitted to PDB ID: PM0077454. The RDRP model predicted with AutoDock3.0.5., a ligand binding site for docking against the antiviral drug Ribavirin. The docked complexes were validated and enumerated using AutoDock to find suitable inhibitors.
Key words: Crimean-Congo hemorrhagic fever virus, RNA-dependent RNA Polymerase, Homology modeling, Ribavirin, Molecular docking.