[Dock-fans] dock6 anion false hits

Hong Liang hongliang.dal at gmail.com
Wed Feb 27 22:05:10 PST 2008

Hi Dock Fans,

I do not understand why Dock6 gave me so many anion hits: false hits.

I prepared the acceptor from sybyl 7.3 (adding hydrogens, applied
kollman_all charge, manually modified the HIS around binding site to their
neutral state.)  I can not see any  positive charged  residues  around the
binding site.  After I docked NCI  compounds  downloaded  from ZINC website,
most of compounds in the top 500 hits are anions.   Based on the biology
test results of some of the anion hits,  those hits are false ones.

The acceptor prepared by Chimera "Dock Prep" tool gave similar docking
result: most of hits are anions.  Did I miss something when I prepared my
grid?  Any feedback is appreciate.


Hong Liang
University of Manitoba
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