Exploring Chemistry Using SMT

Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters

Research output: Contribution to journalConference articleResearchpeer-review

Abstract

How to synthesize molecules is a fundamental and well studied problem in chemistry. However, computer aided methods are still under-utilized in chemical synthesis planning. Given a specific chemistry (a set of chemical reactions), and a specified overall chemical mechanism, a number of exploratory questions are of interest to a chemist. Examples include: what products are obtainable, how to find a minimal number of reactions to synthesize 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.
Original languageEnglish
Book seriesLecture Notes in Computer Science
Volume7514
ISSN0302-9743
DOIs
Publication statusPublished - 2012

Fingerprint

Chemistry
Modulo
Planning
Chemical Synthesis
Chemical compounds
Search Problems
Biosynthesis
Constraint Programming
Expressive Power
Phosphate
Chemical Reaction
Chemical reactions
Pathway
Phosphates
Molecules
Synthesis

Cite this

Fagerberg, Rolf ; Flamm, Christoph ; Merkle, Daniel ; Peters, Philipp. / Exploring Chemistry Using SMT. In: Lecture Notes in Computer Science. 2012 ; Vol. 7514.
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Exploring Chemistry Using SMT. / Fagerberg, Rolf; Flamm, Christoph; Merkle, Daniel; Peters, Philipp.

In: Lecture Notes in Computer Science, Vol. 7514, 2012.

Research output: Contribution to journalConference articleResearchpeer-review

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