ReactionMap: An Efficient Atom-Mapping Algorithm for Chemical Reactions

• Published in: Journal of chemical information and modeling Vol. 53; no. 11; pp. 2812 - 2819
• Main Authors: Fooshee, David, Andronico, Alessio, Baldi, Pierre
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 25.11.2013
• Subjects: Algorithms; Applied sciences; Atoms & subatomic particles; Biochemical Phenomena; Chemical reactions; Chemistry; Computer science; control theory; systems; Data Mining; Data processing. List processing. Character string processing; Databases, Chemical; Exact sciences and technology; General and physical chemistry; General. Nomenclature, chemical documentation, computer chemistry; Genomics; Information retrieval. Graph; Information systems. Data bases; Internet; Memory organisation. Data processing; Models, Chemical; Organic Chemistry Phenomena; Software; Theoretical computing; Theory of reactions, general kinetics. Catalysis. Nomenclature, chemical documentation, computer chemistry; User-Computer Interface; Data analysis; Internet protocol; Very large databases; Minimization; Experimental study; Data mining; Relevance; Chemical reaction; Data integrity; Confidence; Information quality; World wide web; Chemical databasis; Web portal; Subgraph; Random set; Internet; Incomplete information
• ISSN: 1549-9596; 1549-960X; 1549-960X
• DOI: 10.1021/ci400326p

Large databases of chemical reactions provide new data-mining opportunities and challenges. Key challenges result from the imperfect quality of the data and the fact that many of these reactions are not properly balanced or atom-mapped. Here, we describe ReactionMap, an efficient atom-mapping algorithm. Our approach uses a combination of maximum common chemical subgraph search and minimization of an assignment cost function derived empirically from training data. We use a set of over 259,000 balanced atom-mapped reactions from the SPRESI commercial database to train the system, and we validate it on random sets of 1000 and 17,996 reactions sampled from this pool. These large test sets represent a broad range of chemical reaction types, and ReactionMap correctly maps about 99% of the atoms and about 96% of the reactions, with a mean time per mapping of 2 s. Most correctly mapped reactions are mapped with high confidence. Mapping accuracy compares favorably with ChemAxon’s AutoMapper, versions 5 and 6.1, and the DREAM Web tool. These approaches correctly map 60.7%, 86.5%, and 90.3% of the reactions, respectively, on the same data set. A ReactionMap server is available on the ChemDB Web portal at http://cdb.ics.uci.edu.