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Re: Evolutionary algorithm [message #484 is a reply to message #476]

Thu, 07 March 2019 16:25

thomas
Messages: 655
Registered: June 2014

Senior Member

When you have a few active molecules on a given target and intend to search a large compound collection for similar compounds in order to find more potential active ones, then the fastest approach is to use chemical(=graph) similarity of some kind, e.g. the SkeletonSpheres descriptor. Very similar compounds often have similar activities. The drawback of this approach is that this won't do scaffold hopping, which mean that you won't find structures with a substantially different structure core or substitution pattern. The idea of the flexophore (https://pubs.acs.org/doi/abs/10.1021/ci700359j Wink

addresses this issue. It was designed to compare the representative conformer sets of two molecules concerning their protein-binding potential. It classifies atoms that may contribute to binding using PDB statistics. The flexophore considers molecules similar, if they contains atoms that have similar binding behaviour to protein atoms if these atoms' relative 3D orientations are also similar. Depending on the conformational flexibility of individual molecules and the target you may achieve a significantly higher hit rate compared to random or diverse selection, if you preselect screening candidates by flexophore similarity.

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[Message index]

		Evolutionary algorithm By: pc419714@ohio.edu on Tue, 12 February 2019 17:20
		Re: Evolutionary algorithm By: thomas on Tue, 12 February 2019 18:40
		Re: Evolutionary algorithm By: pc419714@ohio.edu on Wed, 13 February 2019 23:05
		Re: Evolutionary algorithm By: pc419714@ohio.edu on Thu, 14 February 2019 04:28
		Re: Evolutionary algorithm By: thomas on Thu, 07 March 2019 16:25
		Re: Evolutionary algorithm By: pc419714@ohio.edu on Thu, 14 March 2019 22:08
		Re: Evolutionary algorithm By: sansun on Sun, 10 May 2020 06:24
		Re: Evolutionary algorithm By: thomas on Sun, 10 May 2020 15:32
		Re: Evolutionary algorithm By: sansun on Wed, 13 May 2020 15:08

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