Phytocompounds as potential antagonists against nsP2 protease of Chikungunya Virus: a multi-faceted molecular modelling approach for drug discovery.
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Jarmani Dansana, Madhusmita Panda, Priyanka Purohit, Abhishikta Gadtya, Bishnupriya Routaray and Biswa Ranjan Meher* Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha-760007, INDIA Email: brm.bot@buodisha.edu.in C478A_APG_In_log_script.zip: Contains docking log files, input scripts, and MD analysis scripts for the C478A mutant with Apigenin. C478A_ISO_In_log_script.zip: Contains docking log files, input scripts, and MD analysis scripts for the C478A mutant with Isorhamnetin. H548A_APG_in_log_script.zip: Contains input and log files for docking and MD simulations of the H548A mutant with Apigenin, including the post-MD analysis script. H548A_ISO_in_log_script.zip: Contains input and log files for docking and MD simulations of the H548A mutant with Isorhamnetin. ligands_mol2_files.zip: 3D molecular structures of ligands in MOL2 format for docking and MD simulations. Ligands_pdb_files.zip: Ligand structures in PDB format used for docking and visualization. Ligands_sdf.zip: Ligands in SDF format obtained form the PubChem database. Prmtop_Inpcrd_all_complexes.zip: Topology (.prmtop) and coordinate (.inpcrd) files for all protein-ligand complexes, used in MD simulations. Protein_wt_Mutants.zip: Includes wild-type nsP2 protease and alanine mutants (C478A and H548A) in PDB format. WT_APG_in_log.zip: Docking input and log files for wild-type nsP2 protease with Apigenin. WT_ISO_IN_LOG.zip: Docking input and log files for wild-type nsP2 protease with Isorhamnetin. Python_script.zip: Contains Python script used for analyzing Principal Component Analysis (PCA) and Dynamics cross correlation matrix (DCCM)
