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Atom mapping with constraint programming

: Mann, M.; Nahar, F.; Ekker, H.; Backofen, R.; Stadler, P.F.; Flamm, C.


Schulte, C.:
Principles and practice of constraint programming. 19th international conference, CP 2013 : Uppsala, Sweden, September 16 - 20, 2013
2013 (Lecture Notes in Computer Science 8124)
ISBN: 3-642-40626-2 (print)
ISBN: 978-3-642-40626-3 (print)
ISBN: 978-3-642-40627-0 (online)
International Conference on Principles and Practice of Constraint Programming (CP) <19, 2013, Uppsala>
Conference Paper
Fraunhofer IZI ()

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.