Molecular modelling and docking analysis study was carried out using AutoDock 4.2 MGL Tools (The Scripps Research Institute, USA) and Pymol Molecular Visualization package (Schrödinger).[4 (link)5 ] Computed Atlas of Surface Topography of Protein (CastP) and FT site open source servers were used to determine the possible binding sites and pocket occupancy of the target protein respectively.[6 (link)7 (link)] The polyphenolic ligands were filtered from Pubchem Database.[8 ] The selected ligands were sketched and converted to their three-dimensional formats using Chemdraw 8.0 and Chemdraw three-dimensional (Cambridge soft. Comp.).[9 (link)] SWISS-MODEL server was used to generate the homology model of target protein.[10 (link)] BLAST server was used to validate the query sequence of the protein.[11 (link)] Procheck server was used to validate the protein by generating Procheck Ramachandran plot (European Bioinformatics Institute, UK).[12 ] DruLiO tool has been used to calculate the drug-likeness of the molecule set.[13 (link)]
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Molecular Docking and Computational Analysis
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- Molecular modelling and docking analysis
- Computed Atlas of Surface Topography of Protein (CastP) and FT site open source servers
- Polyphenolic ligands filtered from Pubchem Database
- SWISS-MODEL server used to generate the homology model of target protein
- BLAST server used to validate the query sequence of the protein
- Procheck server used to validate the protein by generating Procheck Ramachandran plot
- DruLiO tool used to calculate the drug-likeness of the molecule set
- Possible binding sites and pocket occupancy of the target protein
- AutoDock 4.2 MGL Tools (The Scripps Research Institute, USA) and Pymol Molecular Visualization package (Schrödinger) used for molecular modelling and docking analysis
- Chemdraw 8.0 and Chemdraw three-dimensional (Cambridge soft. Comp.) used to sketch and convert the selected ligands to their three-dimensional formats
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