ADL: term"randomized structure"

Richard Wood Richard.Wood at
Fri Mar 25 06:03:07 PDT 2016

Generally, unless one uses a 2-D drawing program, most sketching programs will do some kind of "quick and dirty" optimization.  So, when I said, "non-optimized", that is what I was referring to.  Of course, one can also do a full blown optimization and dock that as well.  

It is probably best to remove the ligand from a ligand-protein crystal structure and re-dock the ligand to see if one can place it in its correct position.  One can then tweak docking parameters to see if they can reproduce the crystal ligand pose.  You can then calculate the RMSD between your docked ligand and that of the crystal structure ligand.  If one is careful, you can get an RMSD of less than 0.5.  (As an aside, I was at an ACS talk a few years back, and there was a speaker from some pharma company who was re-docking ligands and comparing them to the crystal.  He was proud of the fact that his RMSDs were less than 2.  I told him after his talk that he could do much better than that (he I was a lowly post-doc and he was a "professional modeler"-I still remain far below "professional modeler").)

It's questionable how many people actually do that, however.

From: autodock-bounces at [autodock-bounces at] on behalf of Stefano Forli [forli at]
Sent: Thursday, March 24, 2016 8:17 PM
To: autodock at
Subject: Re: ADL: term"randomized structure"

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
> ________________________________________________
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> ________________________________________________
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  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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