[Dock-fans] dock5.3 question!
Le Tien Dung
letiendzung at yahoo.com
Sat Nov 12 00:40:52 PST 2005
I also observed the same phenomenon, however, I think a small difference in scores for different runs is just fine. You should also check if the number of conformations sampling is similar in both batch run and single molecule run. I guess this may also affect the score.
Regarding the IC50 thing, in my opinion, we should not rely much on IC50 but the Ki. This is especially the case when the inhibition is non-complete (partial inhibition). When the inhibition is strong (at very low molar concentration of inhibitors) but it could only inhibit 49% of the total activity when saturated, then we cant find the IC50 value, but we do get the Ki.
Please correct me if I am wrong
ÖEþÀÚ <zxl102623 at 126.com> wrote:
I docked a database today using dock5.3. However, I find energy Score is not uniform with IC50.So I extract one molecular from the database and then docking in the same condition.The result is the energy Score is different from the energy Score in database. Why?
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡zxl102623 at 126.com
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Le Tien Dung, PhD
The Microbial Function Laboratory
National Food Research Institute (NFRI)
Kannondai 2-1-12, Tsukuba, Ibaraki 305-8642 - JAPAN
E-mail: ledt at affrc.go.jp
URLs: http://www.nfri.affrc.go.jp & http://www.cynosura.org (personal)
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