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question about 'analyse similarity/activity cliffs' function [message #588] Thu, 04 July 2019 11:44 Go to next message
alc@sanger.ac.uk is currently offline  alc@sanger.ac.uk
Messages: 3
Registered: July 2019
Location: Cambridge
Junior Member
Hello,
I'm new to DataWarrior and finding it very nice.
I've tried the 'Analyse similarity/activity cliffs' function, and it has made a nice plot showing the molecules as dots.
I can select a molecule and see other similar molecules coloured according to how similar they are to my molecule of interest, using the FragFP score (green: very similar, red: not similar).
I'm wondering is there a way to list the other molecules by their FragFP score from my molecule of interest? The plot I've made contains thousands of molecules, so it's a little hard to see ones that are a bit greenish in the huge plot.
Any advice will be much appreciated!
Regards,
Avril
Re: question about 'analyse similarity/activity cliffs' function [message #595 is a reply to message #588] Tue, 09 July 2019 14:12 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 226
Registered: June 2014
Senior Member
Hi Avril,
the easiest way would be to use a structure filter: right mouse click on a molecule marker of the view, then select 'New Structure Filter From -> this structure'. Then you may adjust the similarity slider in the filter and see the similar molecules in the Table view. To avoid always creating new filters, you may within a view do a right mouse click and 'Copy->Structure as->2D-Structure' and in an existing structure filter double-click the structure and use 'paste' in the editor.

You may also sort the Table/Structure view by a right mouse click on a structure, then 'Sort by->XXX-similarity to this molecule.

Tip: If you calculate the SkeletonSpheres descriptor from your chemical structures with 'Chemistry->From Chemical Structure->Calculate Descriptor->SkelSpheres', you may use this for all chemical similarity functionality, which usually gives better results than the FragFp descriptor.

Hope this helps, Thomas
Re: question about 'analyse similarity/activity cliffs' function [message #620 is a reply to message #595] Wed, 04 September 2019 09:40 Go to previous message
alc@sanger.ac.uk is currently offline  alc@sanger.ac.uk
Messages: 3
Registered: July 2019
Location: Cambridge
Junior Member
Dear Thomas,
I'm sorry for the delay in my reply.
Thank you so much for your helpful reply to my question. I will try out hte SkeletonSpheres descriptor, that ones sounds very interesting to me.
Thank you for making DataWarrior available, it has helped me so much in my work,
Kind Regards,
Avril
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