Searching in Fragment Spaces

The Feature Tree fragment spaces screening concept was exemplified for a number of known actives across different target classes in the paper introducing the general concept [9], Starting from a single active compound as the query structure, the ability of the search method to construct and identify so-called 

The second problem appears when we browse through hit lists resulting from similarity searches in large spaces. Owing to the size of the space, the compounds in the hit list might be very similar to each other. It is therefore necessary to control the diversity within the hit list. Within Feature Trees, we have several criteria at hand for example, the number of common or different fragments between two molecules in the hit list can be limited. Alternatively, Feature Tree similarity within the hit fist can be used to increase diversity. 

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The so-called feature tree fragment space (FTree-FS) method uses dynamic programming techniques and allows the detection of the molecule with the highest similarity to the query that can be found in the fragment space. The efficiency of searches in fragment spaces versus searches in product spaces can be easily shown. 

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