@Article{Mann-CAM-14,
  author = 	 {Martin Mann and Feras Nahar and Norah Schnorr and Rolf Backofen and Peter F. Stadler and Christoph Flamm},
  title = 	 {Atom Mapping with Constraint Programming},
  journal = 	 {BMC Algorithms for Molecular Biology},
  year = 	 {2014},
  volume = 	 {9},
  number = 	 {1},
  pages = 	 {23},
  doi = 	 {10.1186/s13015-014-0023-3},
  issn = 	 {1748-7188},
  user =  	 {mmann},
  note = 	 {In Thematic series on Constraints and Bioinformatics},
  abstract = {  Chemical reactions are rearrangements of chemical bonds.  Each atom in an
  educt molecule thus appears again in a specific position of one of the
  reaction products. This bijection between educt and product atoms is not
  reported by chemical reaction databases, however, so that the 'Atom
  Mapping Problem' of finding this bijection is left as an important
  computational task for many practical applications in computational
  chemistry and systems biology. Elementary chemical reactions feature a
  cyclic imaginary transition state (ITS) that imposes additional
  restrictions on the bijection between educt and product atoms that are
  not taken into account by previous approaches. We demonstrate that
  Constraint Programming is well-suited to solving the Atom Mapping Problem
  in this setting.  The performance of our approach is evaluated for a manually
  curated subset of chemical reactions from the KEGG database featuring various ITS
  cycle layouts and reaction mechanisms.}
}