[Dock-fans] Strange Energy Score(2)

"이주용" nicole23 at naver.com
Mon Jul 18 20:13:57 PDT 2005


Though I wrote down messages also, It didn't delivered -_-; 
 
 I'm trying to do docking experiment with virtual ligands. 
 
 Before docking virtual ligands, I tested DOCK5 program many times with crystal 
structure. Final binding pose was a little bit different from crystal structure. However 
consistant results were obtained from trials which respectively have different random 
seed. 
 
 Since last week I have run DOCK5.2 and I sampled 50 results for each virtual ligands 
because My ligand has many rotatable bond and I thought that I would have so many 
local minimums. By the way, the result was so frustrating. Dock gave me very strange 
Energy Score as you see above thread. The scores range from -60kcal/mol to -4million 
kcal/mol 
 
 I also checked the structure of bounded conformation of protein and ligand but there was nothing strange. Please let me know what's the problem. 
 
P.S) How do you usually choose you parameters? Is there any rules or guidelines for determining the parameters according to size of ligand, structure of ligands? I'm very confused and depressed now...... T.T Please help me~!
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