Rchemcpp: An R package for computing the similarity of molecules

The functionality of Chemcpp is provided in R, that is the computation of similarities between molecules by kernel functions.
The following kernels are implemented:

Input are molecules provided in the SDF format (MOL format) and output is a numeric kernel matrix. This kernel matrix easily be used in R for clustering and prediction tasks, like the prediction of toxicity or biological activity of a given molecule.


G. Klambauer, M. Wischenbart, M. Mahr, T. Unterthiner, A. Mayr, and S. Hochreiter (2015) Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map. Bioinformatics. Advance access: doi: 10.1093/bioinformatics/btv373

Technical Report:


Some benchmarking data sets and R scripts can be downloaded below (will be updated soon):