Publications - Published papers

Please find below publications of our group. Currently, we list 496 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

Atom Mapping with Constraint Programming

Martin Mann, Heinz Ekker, Peter F. Stadler, Christoph Flamm


PREPRINT 12-013: [ PDF ]
[ Publishers's page ]  paperID


In: Proceedings of the Workshop on Constraint Based Methods for Bioinformatics WCB12. Rolf Backofen and Sebastian Will (eds.), Univ. Freiburg 2012, pp. 23-29


The mass flow in a chemical reaction network is determined by the propagation of atoms from educt to product molecules within each of the constituent chemical reactions. The Atom Mapping Problem for a given chemical reaction is the computational task of determining the correspondences of the atoms between educt and product molecules. We propose here a Constraint Programming approach to identify atom mappings for "elementary" reactions. These feature a cyclic imaginary transition state (ITS) imposing an additional strong constraint on the bijection between educt and product atoms. The ongoing work presented here identifies only chemically feasible ITSs by integrating the cyclic structure of the chemical transformation into the search.


bijection, CSP, chemical graph theory