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