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what does it do?

FTrees is a highly efficient software tool for fuzzy similarity searching facilitating virtual HTS. The ability to detect novel molecular scaffolds is one of several features that charaterizes FTrees capabilities.

Its underlying topological descriptor (the Feature Tree) captures connectivity and physico-chemical properties of functional groups. The optimum similarity of two descriptors is defined by an alignment, so an SAR may be readily detected.

FTrees explains similarities to you visually. Two compounds are aligned lightning fast, and distant similarities become obvious.

what's new?

  • super fast, runs in parallel using all the CPUs on your computer
  • no input file size limit, no need to generate FTrees descriptor first
  • beautiful 2D output of molecule-based alignment information
  • returns user defined number of most similar hits
  • super easy-to-use command line interface — try --help to see how it works


FTrees has been reported to be highly successful in numerous projects by various customers in

  1. lead finding,
  2. HTS analysis, and
  3. general virtual screening applications.
scaffold hopping:
Structurally diverse molecules (low fingerprint similarity) may be detected as highly similar Feature Trees
hit rates:
FTrees tops industry standards on a benchmark dataset
mining from the chemical universe:
From billions of virtual yet chemically accessible molecules, find the ones that perform a fuzzy scaffold hop. In minutes. On a simple laptop.


  • Based on a consensus-like scheme, a striking hit rate of 100% has been obtained in three out of four cases with Feature Tree models.
    Read more!
  • We were able to identify interesting new chemical classes in several projects with the FTrees technology, says Karl-Heinz Baringhaus, Sanofi-Aventis.
    Read more!
  • Remarkably, the scaffolds of all solutions as well as their underlying chemistries are quite distinct to those of the query structures, which underscores the strength of the feature tree descriptor in scaffold hopping, Markus Böhm, Pfizer.
    Read more!
  • ...FTrees being seemingly the best general approach of the pure similarity search techniques, Nik Stiefl, Lilly.
    Read more!
  • We have started screening compounds that were selected using FTrees and we found active molecules with unexpected scaffolds — Very exciting!, Wendy Sanderson, Johnson & Johnson.
    Read more!

complementary programs

  • FTrees-FS – the fragment space extension module. Search 1018 compounds in 5 minutes!

application scenarios

What puts FTrees one step ahead of other software in a typical similarity-based virtual screen?

The first thing about the results obtained with FTrees from a chemist's point of view is that the molecules are aligned. That means the chemist can understand why the molecules are awarded a certain similarity. Also, the chemist can influence the alignment — do I want to pick out molecules with a common substructure or molecules with common end groups, similar sized molecules or fragments?

OK, but I want to carry out more complicated experiments — for example, I have several active molecules displaying some diversity, what now?

FTrees is ideal for this scenario. We have already seen how it is possible to align molecules. Let's align the actives; they must have something in common to make them all active. This is possible with the FTrees model building facility. A model is built from a set of several aligned molecules and is in fact itself just another Feature Tree.

So my model tree describes the unified features of my actives but what is this good for?

You can screen with the model Feature Tree just as easily as with a Feature Tree representing a single molecule. That will give just one result set instead of several. The results will highlight compounds that best match the common description of the set of actives.

I work on a daily basis with the in-house database — this contains millions of compounds these days, where do I start?!

Millions of compounds represent no problem to FTrees — 2 million Feature Trees can be handled at once (in memory) by the software. In fact, FTrees is perfect for carrying out data reduction of large datasets. Starting with a small set of seed compounds, you can use FTrees to filter the dataset down to a size more manageable for more intensive modeling methods.

What about fragment-based design?

This is possible with an add-on called FTrees-FS.

download & license


FTrees 3.4 (10.11.2017)
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If you need an older version, please contact us via the support page or email.

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