A Computational Framework for the Discovery of Novel Biotransformations (Final Technical Report for DE-FG02-02ER63457)
- Northwestern Univ., Evanston, IL (United States); Northwestern University
- Northwestern Univ., Evanston, IL (United States)
Development of biotechnologies, such as recombinant DNA and protein engineering, allows us to genetically engineer biological systems for the production of high-value chemicals. Mathematical and computational methods and frameworks are becoming indispensable, powerful tools for gaining a deeper understanding of the function of complex biological systems and for the rational design of genetic and metabolic engineering applications. Under DOE support, a computational framework, the Biochemical Network Integrated Computational Explorer (BNICE), was developed for the construction of metabolic pathways given input substrates and knowledge of enzyme-catalyzed reactions. Graph theory and its associated algorithms are exploited to represent molecules and perform enzyme-catalyzed reactions. Through repetitive application of the set of operators representing the enzymatic reactions of interest to the reactants and their progeny, reaction pathways are generated automatically. The concept of generalized enzyme function is introduced and defined as the third-level enzyme function (EC i.j.k) based on the four-digit transformations of the enzyme classification system (EC i.j.k.l). It maps enzyme-catalyzed reactions to transformations of functional groups and enables the generation of novel species and pathways. The following papers resulted from this grant. The papers that have been published are attached to the end of this report.
- Research Organization:
- Northwestern Univ., Evanston, IL (United States)
- Sponsoring Organization:
- USDOE Office of Energy Research (ER)
- DOE Contract Number:
- FG02-02ER63457
- OSTI ID:
- 968623
- Report Number(s):
- DOE-ER--63457-FINAL
- Country of Publication:
- United States
- Language:
- English
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