ADL: term"randomized structure"

Stefano Forli forli at
Thu Mar 24 18:17:44 PDT 2016

a general practice when testing docking programs is to prevent any kind of bias in the 
input structures that can simplify the search and artificially increase re-docking success 

For this reason, the input structures should be randomized to be different from the 
solution, but still optimized, i.e., all bond angles and lengths must be correct.

The ideal approach would be to generate the 3D coordinates of the ligand starting from 
scratch (e.g., SMILES format) using an external software and dock that.

Although, since during docking bond angles and lengths are not altered, it is sufficient 
to randomize the conformation of the ligand from its experimental coordinates in a 
crystallographic complex, by altering its position, orientation and all the angles in 
rotatable bonds.


On 03/24/2016 06:09 PM, Richard  Wood wrote:
> Non-optimized?
> Richard
> ________________________________________
> From: autodock-bounces at [autodock-bounces at] on behalf of maria timoshik [m.timoshik at]
> Sent: Thursday, March 24, 2016 2:30 PM
> To: autodock at
> Subject: ADL: term"randomized structure"
> Hello:
> I've heard that in a very beginning of video tutorial to Vina Dr. Oleg Todd said:
> "I'll use a randomized structure of a drug molecule".
> What the term RANDOMIZED STRUCTURE actually mean in this context?
> Perhaps professional physico-chemists can explain?
> with regards, Maria
> ________________________________________________
> --- ADL: AutoDock List  --- ---
> ________________________________________________
> --- ADL: AutoDock List  --- ---


  Stefano Forli, PhD

  Assistant Professor of Integrative
  Structural and Computational Biology,
  Molecular Graphics Laboratory

  Dept. of Integrative Structural
   and Computational Biology, MB-112A
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

     tel: +1 (858)784-2055
     fax: +1 (858)784-2860
     email: forli at

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