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.
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..
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
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