Abstract
Chemical reactions can be represented as graph transformations. Fundamental concepts that relate organic chemistry to graph rewriting, and an introduction to the SMILES chemical graph specification language are presented. The utility of both deduction and unordered finite rewriting over chemical graphs and chemical graph transformations, is suggested. The authors hope that this paper will provide inspiration for researchers involved in graph transformation who might be interested in chemoinformatic applications.
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References
Clayden, J., Greeves, N., Warren, S., Wothers, P.: Organic Chemistry. Oxford University Press, Oxford (2000)
Messmer, B.T., Bunke, H.: Subgraph isomorphism in polynomial time. Technical Report IAM 95-003, University of Bern, Institute of Computer Science and Applied Mathematics (1995)
Faulon, J.L.: Automorphism partitioning, and canonical labeling can be solved in polynomial- time for molecular graphs. Journal of Chemical Information and Computer Sciences 38, 432–444 (1998)
Klin, M., Rücker, C., Rücker, G., Tinhofer, G.: Algebraic combinatorics in mathematical chemistry. Methods and algorithms. I. Permutation groups and coherent (cellular) algebras. Technical Report TUM M9510, Techn. Univ. München (1995)
Brickner, S.J., et al.: Synthesis and antibacterial activity of U-100592 and U- 100766, two oxazolidinone antibacterial agents for the potential treatment of multidrug-resistant gram-positive bacterial infections. Journal of Medicinal Chemistry 39, 673–679 (1996)
Garfield, E.: Are you ready for chemical linguistics? Chemical semantics? Chemical semiotics? Or, why WLN? Essays of an Information Scientist 1, 386–388 (1972), Paper available at: http://www.garfield.library.upenn.edu/essays/V1p386y1962-73.pdf
Garfield, E.: Chemico-linguistics: Computer translation of chemical nomenclature. Nature 192 (1961), Paper avilable at http://www.garfield.library.upenn.edu/essays/v6p489y1983.pdf
Weininger, D.: SMILES, a chemical language and information-system. 1. Introduction to methodlogy and encoding rules. Journal of Chemical Information and Computer Sciences 28, 31–36 (1998)
Weininger, D., Weininger, A., Weininger, J.L.: SMILES 2: Algorithm for generation of unique SMILES notation. Journal of Chemical Information and Computer Sciences 29, 97–101 (1989)
Kelley, B.P.: Graph canonicalization. Dr. Dobb’s Journal 28, 66–69 (2003)
Daylight Chemical Information Systems Inc. (Daylight theory manual), Available at http://www.daylight.com/dayhtml/doc/theory/theory.toc.html
Haaksna, A.A., Jansen, B.J.M., de Groot, A.: Lewis acid catalyzed Diels-Alder reactions of S-(+)-carvone with silyloxy dienes. Total synthesis of (+)-small alpha, greek-cyperone. Tetrahedron 48, 3121–3130 (1992)
Smith, W.: Computational complexity of synthetic chemistry – basic facts (1997), Paper available at http://citeseer.ist.psu.edu/192652.html
Corey, E.J., Cheng, X.M.: The Logic of Chemical Synthesis. John Wiley and Sons, Chichester (1995)
Johnson, A., Marshall, C.: Starting material oriented retrosynthetic analysis in the LHASA program. 2. Mapping the SM and target structures. Journal of Chemical Information and Computer Sciences 32, 418–425 (1992)
Rostovtsev, V.V., Green, L.G., Fokin, V.V., Sharpless, K.B.: A stepwise huisgen cycloaddition process: Copper(I)-catalyzed regioselective “ligation” of azides and terminal alkynes. Angewandte Chemie International Edition 41, 2596–2599 (2002)
Bohacek, R.S., McMartin, C., Guida, W.C.: The art and practice of structure-based drug design: A molecular modeling perspective. Medicinal Research Reviews 16, 3–50 (1998)
Lee, D.H., Severin, K., Ghadiri, M.R.: Autocatalytic networks: The transition from molecular self-replication to molecular ecosystems. Current Opinion in Chemical Biology 1, 491–496 (1997)
Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N., Barabási, A.L.: The large-scale organization of metabolic networks. Nature 407, 651–654 (2000)
Jeong, H., Mason, S., Barabási, A.L., Oltvai, N.Z.: Lethality and centrality in protein networks. Nature 411, 41–42 (2001)
Ray, L.B., Jansy, B.R.: Life and the art of networks. Science 301, 1863 (2003)
Benkö, G., Flamm, C., Stadler, P.F.: A graph-based toy model of chemistry. Journal of Chemical Information and Computer Sciences 43, 1085–1093 (2003)
Blostein, D., Fahmy, H., Grbavec, A.: Practical use of graph rewriting. Technical Report 95-373, Queens University (1995)
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Yadav, M.K., Kelley, B.P., Silverman, S.M. (2004). The Potential of a Chemical Graph Transformation System. In: Ehrig, H., Engels, G., Parisi-Presicce, F., Rozenberg, G. (eds) Graph Transformations. ICGT 2004. Lecture Notes in Computer Science, vol 3256. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30203-2_8
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DOI: https://doi.org/10.1007/978-3-540-30203-2_8
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