[Dock-fans] Re: Dock-fans Digest, Vol 17, Issue 10 (orientation number)

Le Tien Dung letiendzung at yahoo.com
Sun Nov 13 17:52:54 PST 2005


Dear Dr. Demetri
   
  Thank you for the useful information regarding the orientation (which I mistakenly named as conformation).
   
  Could you and other Dock-men explain me about the number of orientation that we should try? This is important for me because I do not have a powerful computer to make it sample a number well upon the required values.
   
  Does this value depend upon the nature of of the molecules? (such as the number of heavy atoms). Though I used to set as the default value (500), the dock out file usually gives the values that dock has sampled around 200-300 (in my case).

  Does that value means that 500 orientation sampling is sufficient?
   
  Thank you for your kind reply
   
  Best regards
   
  Le
  
Demetri Moustakas <moustakas at gmail.com> wrote:
  Dear Dr. Zhu,

The reason this sometimes occurs is that DOCK relies upon a random 
number during its use of the simplex minimizer. In the situation you 
described, the random numbers generated while docking the molecule in 
the database will differ from the random nubmers generated while docking 
the molecule alone.

DOCK will generate a set of ligand orientations of the ligand in the 
receptor, which will be identical in your two cases since this step does 
not rely on the RNG. However, once DOCK energy minimizes each of these 
initial orientations, the differences will appear, since the minimzer 
relies on the random numbers. It can be possible that in one case, 
DOCK finds a lower energy minimized ligand pose that the other case 
misses because of the different random numbers.

This is an indication that you are not sufficiently sampling 
orientations of your molecules. If you sample more orientations, you 
will find that these discrepencies go away, since you increase the 
probability of finding the lowest energy poses by starting from more 
initial orientations.

Best,
Demetri Moustakas

> 
> ------------------------------
> 
> Message: 3
> Date: Sat, 12 Nov 2005 09:51:15 +0800
> From: "=?gb2312?B?1uzP/sDa?=" 
> Subject: [Dock-fans] dock5.3 question!
> To: "dock-fans" 
> Message-ID: <200511120151.jAC1pQd00633 at blur.compbio.ucsf.edu>
> Content-Type: text/plain; charset="gb2312"
> 
> Dear sir,
> 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?
> Best wishes
> 
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡
> 
> 
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡xiaolei zhu
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡zxl102623 at 126.com
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-11-12
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Sat, 12 Nov 2005 00:40:52 -0800 (PST)
> From: Le Tien Dung 
> Subject: Re: [Dock-fans] dock5.3 question!
> To: "ÖEþÀÚ" , dock-fans at docking.org
> Message-ID: <20051112084052.79939.qmail at web51407.mail.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> hi there,
> 
> 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 
> 
> Thanks
> 
> Le
> 
> ցEþÀÚ wrote:
> Dear sir,
> 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?
> Best wishes
> 
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡
> 
> 
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡xiaolei zhu
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡zxl102623 at 126.com
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-11-12
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
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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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