title: RxnSim: a tool to compare biochemical reactions.
abstract: : 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.
  
  
  METHODS
  RxnSim is implemented in R and is freely available from the Comprehensive R Archive Network, CRAN (http://cran.r-project.org/web/packages/RxnSim/).
  
  
  BACKGROUND
  anirban.b@samsung.com or ty76.kim@samsung.com
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and.
authors.forename: Varun
authors.initials: V
authors.lastname: Giri
authors.affiliation: Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and.
authors.forename: Tadi Venkata
authors.initials: TV
authors.lastname: Sivakumar
authors.affiliation: Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-do 443803, Korea.
authors.forename: Kwang Myung
authors.initials: KM
authors.lastname: Cho
authors.affiliation: Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-do 443803, Korea.
authors.forename: Tae Yong
authors.initials: TY
authors.lastname: Kim
authors.affiliation: Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and.
authors.forename: Anirban
authors.initials: A
authors.lastname: Bhaduri
mesh_terms: D000465:Algorithms; D001669:Biochemical Phenomena; D062126:Databases, Chemical; D012984:Software