Docking
Zahra Naz
Select the article on docking
• Select article• Read carefully specially about ligand and
target.• Choose target and ligand which you want to
dock
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
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
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
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
Compatibility testing
• Find out whether the selected ligand and protein are compatible to react with one another by using VAMPIRE online software.
Docking server
• Now, its time to dock when compatibility is found successful
• Mostly docking is done by SWISSDOCK server
Find the molecular descriptor values of ligands
• By using medchem designer..
• Complete all tables of requirement and write your article in doc. form
Softwares