Re: [Scaffoldhunter-users] GSOC13 Structure-Activity relationship

[<nl...@us...>]

Hi Srikanth,

SAR is a very general term. It might be more useful to search for "SAR table", 
"SAR Map" or "R-Group table" to get an idea of the concept and variations.

A straight forward approach is to start with a SAR table for a single 
scaffold. Each row represents a molecule and there are columns for each 
substitution site and each property of the molecule. This would already be 
very useful when linked to the Scaffold Tree View.
However, the problem becomes more challenging when molecules with different 
scaffolds should be depicted in the same table. The second article (Clark & 
Labute) listed at the ideas page deals with this problem from the molecular 
structure point of view. However, I think a less sophisticated approach should 
be sufficient for the project idea. You may think about the following  
challenging questions:

  * Is there a viable simple approach to assign scaffolds/substitution sites
    for the case of molecules with different scaffolds? An approach different
    from the one described in the article would be to identify a common core
    of all molecules (e.g., based on their maximum common subgraph, a
    functionality provided by the toolkit CDK). However, this is computational
    demanding and the core typically does not comply with the scaffolds
    contained in the scaffold tree view. Can views be linked in a meaningful
    way in this case?

  * Assume only scaffolds according to the scaffold tree are generated and one
    scaffold is an ancestor of a different scaffold in the tree. Can this 
    relation be visualized in the SAR table view? Can both views be linked in
    a way such that their relation becomes clear?

  * If we have multiple scaffolds and multiple substitution sites, how to
    visualize them in one table? One approach would be to generate a table,
    where each row represents a scaffold and each column a specific substitute
    for a single user-selected substitution site. Then each cell may represent 
    multiple molecules (differing at the other substitution sites). How to
    visualize the property values of multiple molecules in one cell?



Regards,

  Nils


On Tuesday 23 April 2013 11:44:56 srikanth bezawada wrote:
> Hello Karsten and Nils, Thanks for your reply!
> 
> 
>         Karsten, I have started exploring more about SAR to get
> familiar with it and I'll post if I get doubts . Please do point me
> any more specific links if I should refer  regarding SAR. Once I'm
> done with basics of SAR, we can discuss regarding how end user must
> visualize (or) work with the table view.
> 
>         Nils, Thanks for pointing me towards required sourcecode to be
> concentrated upon. Since the project idea is straight forward, what
> key points can i include in my proposal, so as to send ahead something
> strong and concrete ? .
> 
> 
> 
> Thanks,
> Srikanth.