Improved automated reaction mapping

Authors:
Tina Kouri;Dinesh Mehta
Affiliations:
Colorado School of Mines;Colorado School of Mines
Venue:
SEA'11 Proceedings of the 10th international conference on Experimental algorithms
Year:
2011

Citing 5
Cited 0

Computers and Intractability; A Guide to the Theory of NP-Completeness

Computers and Intractability; A Guide to the Theory of NP-Completeness
Canonical labeling of graphs

STOC '83 Proceedings of the fifteenth annual ACM symposium on Theory of computing
Computational Discrete Mathematics: Combinatorics and Graph Theory with Mathematica ®

Computational Discrete Mathematics: Combinatorics and Graph Theory with Mathematica ®
Improved random graph isomorphism

Journal of Discrete Algorithms
Automated reaction mapping

Journal of Experimental Algorithmics (JEA)

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Abstract

Automated reaction mapping is an important tool in cheminformatics where it may be used to classify reactions or validate reaction mechanisms. The reaction mapping problem is known to be NP-Complete and may be formulated as an optimization problem. In this paper we present three algorithms that continue to obtain optimal solutions to this problem, but with significantly improved runtimes over the previous CCV algorithm. Our algorithmic improvements include (a) the use of a fast (but not 100% accurate) canonical labeling algorithm, (b) name reuse (i.e., storing intermediate results rather than recomputing), and (c) an incremental approach to canonical name computation. Experimental results on chemical reaction databases demonstrate our 2-CCV NR FDN algorithm usually performs over ten times faster than previous fastest automated reaction mapping algorithms.