Article open access publication

Atom mapping with constraint programming

Algorithms for Molecular Biology, Springer Nature, ISSN 1748-7188

Volume 9, 1, 2014

DOI:10.1186/s13015-014-0023-3, Dimensions: pub.1005738442, PMC: PMC4256833, PMID: 25484913,


Mann, Martin * (1)
Backofen, Rolf (1) (2)
Stadler, Peter F (3) (4) (5) (6) (7)

* Corresponding author



  1. (1) University of Freiburg, grid.5963.9
  2. (2) University of Copenhagen, grid.5254.6, KU
  3. (3) Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, , , Leipzig 04107, Germany, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany
  4. (4) Fraunhofer Institute for Cell Therapy and Immunology, grid.418008.5
  5. (5) Max Planck Institute for Mathematics in the Sciences, grid.419532.8
  6. (6) Santa Fe Institute, grid.209665.e
  7. (7) University of Vienna, grid.10420.37


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.


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