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Exploring Chemistry using SMT

Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters

submitted to:
Principles and Practice of Constraint Programming (CP) 2012

How to synthesize molecules is a fundamental and well studied problem in chemistry. However, computer aided methods are still under-utilized in the chemical reaction planning. Given a specific chemistry, i.e. a set of real world chemical reactions, and a chemical mechanism with possibly unspecified molecules, a number of explorative questions are of interest to a chemist. Examples include what products are obtainable, how to reach a minimal number of reactions to achieve a certain chemical compound, and how to map a specific chemistry to a mechanism. We present a Constraint Programming based approach to these problems and employ the expressive power of Satisfiability Modulo Theory (SMT) solvers. We show results for an analysis of the Pentose Phosphate Pathway and the Biosynthesis of 3-Hydroxypropanoate. The main novelty of the paper lies in the usage of SMT for expressing search problems in chemistry, and in the generality of its resulting computer aided method for synthesis planning.

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