Atom Mapping with Constraint Programming

  • Martin Mann
  • Feras Nahar
  • Heinz Ekker
  • Rolf Backofen
  • Peter F. Stadler
  • Christoph Flamm
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8124)


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.


Atom Mapping Constraint Program Constraint Satisfaction Problem Reaction Mapping Product Graph 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Martin Mann
    • 1
  • Feras Nahar
    • 1
  • Heinz Ekker
    • 5
  • Rolf Backofen
    • 1
    • 2
    • 3
    • 4
  • Peter F. Stadler
    • 5
    • 6
    • 7
    • 8
    • 9
  • Christoph Flamm
    • 5
  1. 1.Bioinformatics, Department for Computer ScienceUniversity of FreiburgFreiburgGermany
  2. 2.Centre for Biological Signalling Studies (BIOSS)University of FreiburgGermany
  3. 3.Centre for Biological Systems Analysis (ZBSA)University of FreiburgGermany
  4. 4.Center for non-coding RNA in Technology and HealthUniversity of CopenhagenDenmark
  5. 5.Institute for Theoretical ChemistryUniversity of ViennaViennaAustria
  6. 6.Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for BioinformaticsUniversity of LeipzigLeipzigGermany
  7. 7.Max Planck Institute for Mathematics in the SciencesLeipzigGermany
  8. 8.Fraunhofer Institute for Cell Therapy and ImmunologyLeipzigGermany
  9. 9.Santa Fe InstituteSanta FeUSA

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