Drawing Similar Compounds in 2D Using Feature Tree Mappings

Drawing Similar Compounds in 2D Using Feature Tree Mappings 

For drawing similar molecules in a similar way, the Feature Tree comparisons are useful as they detect similarity beyond mere substructure identity and they also provide a mapping that can be viewed as alignments of molecule fragment pairs. 

The directions for the extracted bond paths in the current molecule are taken from the template and used as directional constraints for the drawing algorithm. 

In Fig. 4.17, a set of benzodiazepines is shown that were aligned using Feature Tree matchings. The bond orientations extracted from the template are shown by arrows. The algorithm has been shown to be very useful to visualize similarities beyond common subgraphs. Further test cases can be found in [53]. 

We would like to thank Dirk Tomandl (Santhera Pharmaceuticals) for stimulating discussions, molecular framework analysis and cheminformatics support. Thanks are also due to Marcus Gastreich (BioSolvelT) for his assistance in the CDK2 virtual screening experiment and for his general advice on chemistry matters. Finally we would like to thank Christian Lemmen (BioSolvelT) for many valuable suggestions on the manuscript. 

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