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pharmacophore-style similarity for scaffold hopping

what does it do?

Feature Trees (short FTrees) is a highly efficient software tool for pharmacophore-style similarity searching, facilitating virtual HTS. The Feature Tree descriptor captures a molecule's overall topology and its pharmacophore properties. The similarity of two such descriptors is based on an alignment (shown above by the color-coding of related functional groups).

Through it's fuzziness, the ability to detect novel molecular scaffolds is one of several strengths of FTrees.

The picture above shows two PAF antagonists that structurally do not look alike. Even a very experienced medicinal chemist would probably not have picked the molecule on the right, based on the information of the molecule on the left. Comparing the feature tree representation however, the similarity is striking. Look at the colors of the individual nodes, where same color shares similar properties, then you will understand how FTrees aligns these molecules, and why it considers these two as similar.

FTrees ranks the molecule on the right #5 with the one on the left as query. Standard 2D methods rank this compound very low[1]. Read more about it in the science section.


What is the competitive advantage of FTrees over other similarity calculators?

I already have several descriptors in my portfolio. Why do I need another one?

My in-house database contains millions of compounds. Can FTrees handle that?

Several millions of molecules is a lot. So how fast is it really?

[1] Hans Briem, Uta F. Lessel
In vitro and in silico affinity fingerprints: Finding similarities beyond structural classes.
Perspectives in Drug Discovery and Design, 2000, 20 (1), 231-244
[2] Thierry Kogej, Ola Engkvist, Niklas Blomberg, Sorel Muresan
Multifingerprint based similarity searches for targeted class compound selection.
Journal of Chemical Information and Modeling, 2006, 46 (3), 1201-1213
[3] Markus Böhm, Tong-Ying Wu, Holger Claußen, Christian Lemmen
Similarity Searching and Scaffold Hopping in Synthetically Accessible Combinatorial Chemistry Spaces.
Journal of Medicinal Chemistry, 2008, 51 (8), 2468-2480