fmcsR: Mismatch Tolerant Maximum Common Substructure Searching in R
I’m not a big user of R a free software environment for statistical computing and graphics, but occasionally I notice cheminformatics modules being published. The latest issue of Bioinformatics DOI has a paper describing “fmcsR: Mismatch Tolerant Maximum Common Substructure Searching in R”.
The fmcsR package provides an R interface, with the time consuming steps of the FMCS algorithm implemented in C++. It includes utilities for pairwise compound comparisons, structure similarity searching, clustering and visualization of MCSs. In comparison to an existing MCS tool, fmcsR shows better time performance over a wide range of compound sizes. When mismatching of atoms or bonds is turned on, the compute times increase as expected, and the resulting FMCSs are often R1C5 substantially larger than their strict MCS counterparts. Based on R1C6 extensive virtual screening (VS) tests, the flexible matching feature enhances the enrichment of active structures at the top of MCS-based similarity search results. With respect to overall and early enrichment performance, FMCS outperforms most of the seven other VS methods considered in these tests.
fmcsR is freely available for all common operating systems from the Bioconductor site http://www.bioconductor.org/packages/devel/bioc/html/fmcsR.html.