I found that almost all the docking tools including Rosseta try to use the entire carbohydrate molecules for docking, but in fact from many X-ray crystal stuctures we found that if a carbohydrate molecules contains three or four ring, it usually just use the one terminal ring to form some H-bond with the protein. For such case, Glide or other tools would very difficult to get a reliable docking results.
Rosetta coupled with other docking tools tend to dock the oligosaccride with full molecule, does this mean that current docking tools emphasize too much on enthalpy calculation while the entropy calculation is inefficient? In this case, leaving some rings of oligosaccride in solvent would be considered unfavorable by the docking tools. How do you think of this?
I would be very appreciated if someone could give me some advices on how to avoid Rosseta use the entire carbohydrate for docking and how to get a much more reliable results for carbohydrate docking?
Thank you very much