Autodock Vina Tutorial - Molecular Docking

#Protein #Structure #Analysis #Bioinformatics #Protein #Ligand #Inhibitor

Blog: https://farhanhaqjahangiri.blogspot.com/2022/09/a-complete-guide-for-autodock-vina.html

1. Download and install MGL Tools (http://mgltools.scripps.edu/downloads)
2. Run the setup , it will take few minutes.
3. After that download AUTODOCK Vina and PYMOL using these links http://vina.scripps.edu/index.html
https://pymol.org/2/
4. AUTODOCK is used for molecular docking, in which we search for the appropriate ligand for the protein.
5. RCSB PDB Database is used for PDB structures of the proteins and PubChem used for downloading the Ligand.
6. Open the protein structure in AUTODOCK Tools.

7. Now you need to prepare the protein to interact with the ligand.
8. Delete all the water molecules from the structure and add polar hydrogen residues .
9. Now add kollman charges to have a best possible protein ligand interaction.
10. Convert SDF File into PDB to load it in AUTODOCK Tool using PYMOL.
11. Prepare the ligand file by following the steps.
12. Prepare the Grid, load the protein file and a ligand file.
13. Open the Grid box, it will show exact location where the docking will take place.
14. Open the command line, give it the path of your folder file.
15. Prepare config.txt file to have all the dimensions.
16. Now run the command
17. It will generate the log.txt file which will tell the docking score