Noushin Hadadi

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Because the complexity of metabolism cannot be intuitively understood or analyzed, computational methods are indispensable for studying biochemistry and deepening our understanding of cellular metabolism to promote new discoveries. We used the computational framework along with cheminformatic tools to assemble the whole theoretical reactome from(More)
Mono-ethylene glycol (MEG) is an important petrochemical with widespread use in numerous consumer products. The current industrial MEG-production process relies on non-renewable fossil fuel-based feedstocks, such as petroleum, natural gas, and naphtha; hence, it is useful to explore alternative routes of MEG-synthesis from gases as they might provide a(More)
Reaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely available in the literature. The understanding of metabolic pathways at the atomic level is of great(More)
Lipids are important compounds for human physiology and as renewable resources for fuels and chemicals. In lipid research, there is a big gap between the currently available pathway-level representations of lipids and lipid structure databases in which the number of compounds is expanding rapidly with high-throughput mass spectrometry methods. In this work,(More)
Designing putative metabolic pathways is of great interest in synthetic biology. Retrobiosynthesis is a discipline that involves the design, evaluation, and optimization of de novo biosynthetic pathways for the production of high-value compounds and drugs from renewable resources and natural or engineered enzymes. The best candidate pathways are then(More)
The present work is part of a series of papers aiming at a thorough understanding of the thermodynamics of metabolism over a broad range of external conditions. The focus here is on the systematic study of solvation/hydration of a variety of fluids via an equation-of-state approach. This approach permits the study not only of the overall free energy,(More)
The present work is the first of a series of papers aiming at a coherent and unified development of the thermodynamics of metabolism and the rationalization of feasibility analysis of metabolic pathways. The focus in this part is on high-level quantum chemical calculations of the thermochemical quantities of relatively heavy metabolites such as amino(More)
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