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Generic strategies for chemical space exploration
by Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler
International Journal of Computational Biology and Drug Design (IJCBDD), Vol. 7, No. 2/3, 2014
Abstract: The chemical universe of molecules reachable from a set of start compounds by iterative application of a finite number of reactions is usually so vast, that sophisticated and efficient exploration strategies are required to cope with the combinatorial complexity. A stringent analysis of (bio)chemical reaction networks, as approximations of these complex chemical spaces, forms the foundation for the understanding of functional relations in Chemistry and Biology. Graphs and graph rewriting are natural models for molecules and reactions. Borrowing the idea of partial evaluation from functional programming, we introduce partial applications of rewrite rules. A framework for the specification of exploration strategies in graph-rewriting systems is presented. Using key examples of complex reaction networks from carbohydrate chemistry we demonstrate the feasibility of this high-level strategy framework. While being designed for chemical applications, the framework can also be used to emulate higher-level transformation models such as illustrated in a small puzzle game.
Online publication date: Tue, 27-May-2014
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