I have a molecule (which in pdb is complexed with many ligands). I want to remove those ligans to try to see where and if my own inhibitors will bind to the receptor. Since i don't know which active sites there will be, I will need to carry out an exhaustive search. How do I go about it? Do I have to enter coordinates for each residue and run the docking 529 times (my residue number of the protein)? I'm very new to this field.
Try Q-site finder for getting Ligand bind pockets in your protein. Alternatively you can search literature on your protein for potential Allosteric sites which might be available.
Then you can use these info to do docking studies of your inhibitors with AUTODOCK vina.
You can also try a whole protein search with Autodock Vina. Try with a moderate exhaustiveness (>15) and then recheck this results with smaller search boxes. Vina has done a good work in the test I've done, so it should work for you as well. If you don't know how to use vina, you can look for the tutorial, search in the forums of the scripps institute, or ask again.
@ Madhulika, first of all i would like to know is this your protein is a experimental pdb structure like -X-RAY, NMR etc or Homology model? if it is experimental pdb structure, In their published article they must have mentioned about active site residues else you can find from FTMAP. and if it is model structure you can try Q-site finder or CastP server for active site.
U can Try Molegro Virtual Docking Software Which Easily helps you to find out the active sites (Cavity detection) where exactly the ligand binds
You can try the Various tools such as CastP, Q-site finder, PASS to find the binding site of the receptor protein. Among them one site might be the active site. so, to make sure the specific site for docking you can compare the results of the many tools and try to find the common site between the tools and then you can go for the docking of the Inhibitors.
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