I am working on small molecules docking in Glide. From crystallographic data I noticed that my ligands make an important salt bridge with ASP amino acid residue in a receptor. I have noticed that I can make positional, hydrophobic and hydrogen bond constraints in Glide, but I couldn't find a salt bridge constraint.
I would appreciate any suggestions, since setting this constraint will improve my selection of candidates.
Hai,
I have tried the same when I was targeting a specific salt bridge between ASP and ARG/LYS. But simply docking the different conformers of your small molecule near the targeted site will achieve it.
You have to first locate the position of your important salt bridge in the protein. Then just try re-docking with the small molecules you have in the co-crystallized ligand position. Then check the 2-D ligand interaction diagram.
Good Luck
Salt bridge is a covalent bond like, so you should be sure that the docking method you use can be able to consider such a connection or not between the ligand and protein atoms.
Regarding to the having crystallographic data from the target- ligand complex, it seems that docking method could not be a useful technique for your work. You do not need any prediction, it is previously confirmed where your ligand bound. Thus, I suggest to used Discovery Studio 4.5 to create your complex favorably according to the crystallography.
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