@InProceedings{Mann_atommapping_13,
  author = 	 {Martin Mann and Feras Nahar and Heinz Ekker and Rolf Backofen and Peter F. Stadler and Christoph Flamm},
  title = 	 {Atom Mapping with Constraint Programming},
  booktitle={Proc. of the 19th International Conference on Principles and Practice of Constraint Programming (CP'13)},
  series={LNCS},
  publisher={Springer},
  year = 	 {2013},
  pages = 	 {805-822},
  volume = 	 {8124},
  doi = 	 {10.1007/978-3-642-40627-0_59},
  location =     {Uppsala, Sweden},
  editor = 	 {C. Schulte},
  isbn = 	 {978-3-642-40626-3},
  user = 	 {mmann},
  abstract= 	 {Chemical reactions consist of a rearrangement of bonds so that each atom
  in an educt molecule appears again in a specific position of a reaction
  product. In general this bijection between educt and product atoms is not
  reported by chemical reaction databases, leaving the Atom Mapping Problem
  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 subset of chemical reactions from the KEGG database featuring various
  ITS cycle layouts and reaction mechanisms.}
}