Docking studies

1. Docking
Zahra Naz

2. Select the article on docking
• Select article
• Read carefully specially about ligand and
target.
• Choose target and ligand which you want to
dock

4. Finding of a ligand
• Suppose, you want to work on a drug to treat
cancer, search for a chemical of plant or
microbial origin
• Then find the target of this ligand

5. Get it be finalized by Instructor
The selected ligands and compounds must b
unique or novel and no research work would
be done on these in the way you want to work

6. Find out softwares
• Try to use those softwares which have been
used in selected article.
• E.g. for 3D images, C3nD software can be used
• For pdb files, swiss pdb viewer is used

7. Retrieving sequences and structures
• Use NCBI website for getting information
about your target
• Pubchem is helpful for obtaining ligand files in
desired format
• ZINC12 is used to find ligand structure for
docking with the help of ligand’s pubchem id

13. Compatibility testing
• Find out whether the selected ligand and
protein are compatible to react with one
another by using VAMPIRE online software.

16. Docking server
• Now, its time to dock when compatibility is
found successful
• Mostly docking is done by SWISSDOCK server

20. Find the molecular descriptor values of
ligands
• By using medchem designer..

23. • Complete all tables of requirement and write
your article in doc. form

25. Softwares