[Dock-fans] how select active site manually from cluster

Pawan Gupta pawanguptainfo at yahoo.co.in
Tue Jul 6 23:51:29 PDT 2010


I beginner of  Dock program. 

Sir I have gone through the tutorial which you given on your site, one problem i 
faced during the tutorial that i did not able to select the active site manually 
even-if my protein did not have co-crystallized ligand.
I know the active site center coordinate (XYZ) which is give my receptor_noH.pdb 
file.

How to select active site residues?

Tell how to dock the molecules in solvation state of protein and what is the 
significance of it from normal docking?

I did not find any tutorial regarding solvation docking.

which score is better ?

i calculated contact socre, but how i analyaze the score 

thanks in advance

Pawan Gupta
PhD scholar
NIPER, Mohali, India.

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