RxnSim: A tool to compare biochemical reactions

Abstract

Summary: Quantitative assessment of chemical reaction similarity aids database searches, classification of reactions and identification of candidate enzymes. Most methods evaluate reaction similarity based on chemical transformation patterns. We describe a tool, RxnSim, which computes reaction similarity based on the molecular signatures of participating molecules. The tool is able to compare reactions based on similarities of substrates and products in addition to their transformation. It allows masking of user-defined chemical moieties for weighted similarity computations. Availability and implementation: RxnSim is implemented in R and is freely available from the Comprehensive R Archive Network, CRAN (http://cran.r-project.org/web/packages/RxnSim/).