Molecular Docking of Silibinin and Chalcone
Corresponding Organization :
Other organizations : Islamic Azad University, Science and Research Branch, University of Tehran, Tehran University of Medical Sciences
Variable analysis
- Molecular docking using Autodock Vina software
- Energy minimization using Avogadro software
- Binding affinity between ligands (silibinin and trans-chalcone) and proteins (natural and denatured insulin structures)
- Molecular structures of silibinin and trans-chalcone obtained from PubChem
- Natural (3I40) and denatured (1SF1) insulin structures obtained from RCSB protein database
- Removal of water molecules from crystal structures
- Addition of polar hydrogens and Gasteiger charges to ligands and proteins using Autodock Tools software
- Consideration of all rotating bonds of the active ligands
- Blind docking with a large enough search space to cover the entire protein surface
- Visualization of 2D protein-ligand interactions using LIGPLOT software
- Visualization of 3D images using VMD software
Annotations
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