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:
the marginalized graph kernel between labeled graphs
extensions of the marginalized kernel
graph kernels based on tree patterns
kernels based on pharmacophores for 3D structure of molecules
Paper under preparation:
Michael Mahr, Günter Klambauer, Sepp Hochreiter.
"Rchemcpp: an R package for computing the similarity of molecules".
Technical Report (available soon):
- Download the source package available from Bioconductor:
Rchemcpp R package
- A web service for finding structural analogs using Rchemcpp is online:
Finding analogs in ChEMBL - Similarity Search with Rchemcpp
Some benchmarking data sets and R scripts can be downloaded below (will be updated soon):
mutag.sdf (0.4 MB)