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8841 Views 8 Replies Latest reply: Sep 19, 2011 8:22 AM by Georgi Chankov RSS Branched to a new discussion.
New User 8 posts since
Dec 29, 2010
Currently Being Moderated

Dec 14, 2011 10:25 AM

Chemical Similarity

For the newest version of the Toolbox, is there a documented process to use the toolbox to determine if new chemical could be added to a pre-existing group of chemicals for read across assessment?

 

Put a more practical way,  I have a file containing approx 30 chemicals that have been grouped and I would like to load into the toolbox (which I can do).  I would then like to compare new chemicals to the group by Similarity to see if the new chemical can be added to the group.  I would like to do all of this inside the toolbox if possible.

 

Can you guide me as to how this can be done?

 

Thanks.

  • Geoffrey Hynes New User 48 posts since
    Nov 16, 2010
    Currently Being Moderated
    Sep 8, 2011 4:32 PM (in response to Greg Dameron)
    Chemical Similarity

    Hi Greg,

     

    If you highlight only your created database containing the 30 substances, no other stuctures or data will be returned or interrogated. Therefore the new structure will be compared only to your specific database.

    I have completed a similar assessment with success.

    Geoff...

  • Bob DIDERICH Apprentice 177 posts since
    Jan 15, 2010
    Currently Being Moderated
    Sep 8, 2011 4:34 PM (in response to Greg Dameron)
    Chemical Similarity

    Hi Greg,

     

    You can do this by building a profiler.

     

    There is some general guidance on building profilers here:

     

    http://oasis-lmc.org/toolbox/PPT/Tutorial8.ppt

     

    and

     

    http://oasis-lmc.org/toolbox/Demo4/

     

    I suspect you will have to do this by defining the level of similarity to each of your 30 chemicals.

     

    In addition I would recommend that you also define your similarity based on the profiling results which are common to all the members of the group.

     

    You can then run your new profiler on any list of chemicals and find chemicals which potentially belong to your group.

     

    Hope this helps

     

    Bob

    • Bob DIDERICH Apprentice 177 posts since
      Jan 15, 2010
      Currently Being Moderated
      Sep 9, 2011 2:48 PM (in response to Greg Dameron)
      Chemical Similarity

      I don't think you can load a list of chemicals into your custom profiler.

       

      You will have to define the similarity rules against each and every chemical in your group and then logically group them, e.g.

       

      >50% similarity with chemical 1 from your group AND >50% similarity with chemical 2 from your group AND ...

       

      But once again, as I mentioned above, it might make more sense not to build your profiler based on mathematical structural similarity, but according to the commonalities in structure in your group as well as the results from the other profilers, e.g.

       

      Aromatic (according to organic functional groups) AND Schiff base former according to Protein binding by OASIS AND...

       

      Bob

    • Georgi Chankov New User 61 posts since
      May 11, 2010
      Currently Being Moderated
      Sep 19, 2011 8:22 AM (in response to Greg Dameron)
      Chemical Similarity

      I logged the "list index out of bounds" error to our bug tracking database. We'll look into it.

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