Question: Protein Protein Docking
gravatar for srikrish.sree
8.3 years ago by
srikrish.sree20 wrote:

my protein is glycosylated at 2 residues. I want to include the glycosylation during docking since the ligand (Peptide) binds to the glycosylated protein more efficiently that the non-glycosylated form. Most docking servers donot recognise the glycosylation during docking. I want to know about the docking platforms available for protein protein docking which recognises the glycosylation in proteins.

Also pls advice on how to visualise the possible interactions between the protein and the ligand (peptide) after docking.

docking • 3.1k views
ADD COMMENTlink written 8.3 years ago by srikrish.sree20
gravatar for João Rodrigues
8.3 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

As I mentioned in your other thread, you need to build a topology for your glycosylated ligand. If you do not provide a topology and parameters for that particular glycosylated residue, the program will not be able to interpret it in terms of forcefield (ie. bond lengths, angles, partial charges, etc). You can build one using PRODRG, ACPYPE, or the GLYCANS server. For example, the HADDOCK webserver will automatically build a topology for any HETATM that it doesn't recognize, by querying PRODRG. It's not your best option, but it's a start. You can also download the program and then feed it your own topology, in whatever way it was built, provided it's in the right format (CNS).

Regarding other docking programs, like Autodock, the procedure is probably similar but I haven't got experience with them..

ADD COMMENTlink modified 8.3 years ago • written 8.3 years ago by João Rodrigues2.5k

Mr. Rodrigues, thansk for your answer. Actually, I had created the glycosylated protein using GLYPROT. I am not sure if GLYPROT creates its own topology. Any ways, i will start creating it using PRODRG or GLYCANS as you suggested. Hope I can buzz you if i have any questions on the same. Thanks

ADD REPLYlink written 8.3 years ago by srikrish.sree20
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