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FTrees-FS is the combinatorial fragment space extension module to FTrees, our fast similarity-based search engine.

The underlying concept is strikingly easy: instead of searching already "assembled" molecules, FTrees instead performs a combinatorial build-up of compounds from "fragments". Sources of fragments can be either combinatorial libraries or any fragment-generating procedure.

With FTrees-FS you can perform the fragment assembling steps and at the same time make use of the search/comparison/screening facilities on the level of Feature Tree similarity. Recent applications have demonstrated searches in spaces large as 1017.

recent publications and presentations

status and availability

FTrees-FS is available as a modular extension of FTrees.


No matter how big your in-house library and no matter how many compounds you acquire to add to it, it will only be a tiny fraction of what your chemists are capable of synthesizing.
download KnowledgeSpace
Fragments + Reactions = 12,000,000,000 Synthesizable(!) Compounds

Now you have the possibility of searching incredibly large numbers of molecules in a sensible way: Compounds you find can actually be made! Search our new, free KnowledgeSpace – within just minutes!

The KnowledgeSpace (Version 1.0) has been compiled based on 82 synthesis protocols from the literature. Some are target-specific (GPCRs, proteases, kinases, ...), and some are purely chemistry-driven. Altogether they cover 10,879 unique fragments and comprise about 12,000,000,000 virtual products.

The KnowledgeSpace has been tested to retrieve known drugs and drug like molecules. See the details of some work in a presentation which used FTrees-FS.

The KnowledgeSpace is ready to use for FTrees-FS searches. It can be easily uploaded into related Pipeline Pilot® and KNIME® components.


stay tuned with all the breaking news.


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