Chapter

Principles and Practice of Constraint Programming

Volume 8124 of the series Lecture Notes in Computer Science pp 805-822

Atom Mapping with Constraint Programming

  • Martin MannAffiliated withBioinformatics, Department for Computer Science, University of Freiburg
  • , Feras NaharAffiliated withBioinformatics, Department for Computer Science, University of Freiburg
  • , Heinz EkkerAffiliated withInstitute for Theoretical Chemistry, University of Vienna
  • , Rolf BackofenAffiliated withBioinformatics, Department for Computer Science, University of FreiburgCentre for Biological Signalling Studies (BIOSS), University of FreiburgCentre for Biological Systems Analysis (ZBSA), University of FreiburgCenter for non-coding RNA in Technology and Health, University of Copenhagen
  • , Peter F. StadlerAffiliated withInstitute for Theoretical Chemistry, University of ViennaBioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of LeipzigMax Planck Institute for Mathematics in the SciencesFraunhofer Institute for Cell Therapy and ImmunologySanta Fe Institute
  • , Christoph FlammAffiliated withInstitute for Theoretical Chemistry, University of Vienna

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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.