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Consistent estimation of Gibbs energy using component contributions
Standard Gibbs energies of reactions are increasingly being used in metabolic modeling for
applying thermodynamic constraints on reaction rates, metabolite concentrations and kinetic …
applying thermodynamic constraints on reaction rates, metabolite concentrations and kinetic …
In silico cell factory design driven by comprehensive genome-scale metabolic models: Development and challenges
Genome-scale metabolic models (GEMs) have been widely used to design cell factories in
silico. However, initial flux balance analysis only considers stoichiometry and reaction …
silico. However, initial flux balance analysis only considers stoichiometry and reaction …
An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
Motivation: The laws of thermodynamics describe a direct, quantitative relationship between
metabolite concentrations and reaction directionality. Despite great efforts, thermodynamic …
metabolite concentrations and reaction directionality. Despite great efforts, thermodynamic …
Estimating metabolic equilibrium constants: progress and future challenges
Reaction equilibrium constants (K eq s) are key parameters that impose thermodynamic
constraints on the function of a metabolic network. An important approach for K eq …
constraints on the function of a metabolic network. An important approach for K eq …
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design
Group contribution (GC) methods are conventionally used in thermodynamics analysis of
metabolic pathways to estimate the standard Gibbs energy change (Δ r G′ o) of enzymatic …
metabolic pathways to estimate the standard Gibbs energy change (Δ r G′ o) of enzymatic …
Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction
Reaction directionality is a key constraint in the modeling of genome-scale metabolic
networks. We thermodynamically constrained reaction directionality in a multicompartmental …
networks. We thermodynamically constrained reaction directionality in a multicompartmental …
How important is thermodynamics for identifying elementary flux modes?
We present a method for computing thermodynamically feasible elementary flux modes
(tEFMs) using equilibrium constants without need of internal metabolite concentrations. The …
(tEFMs) using equilibrium constants without need of internal metabolite concentrations. The …
A toolbox for develo** bioinformatics software
K Rother, W Potrzebowski, T Puton… - Briefings in …, 2012 - academic.oup.com
Creating useful software is a major activity of many scientists, including bioinformaticians.
Nevertheless, software development in an academic setting is often unsystematic, which can …
Nevertheless, software development in an academic setting is often unsystematic, which can …
Protocols for calculating reaction kinetics and thermodynamics
Thermodynamics is central to our understanding of the ecology and physiology of microbial
ecosystems. In physiological research, thermodynamics is used to determine the …
ecosystems. In physiological research, thermodynamics is used to determine the …
Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions
Motivation Accurate and wide-ranging prediction of thermodynamic parameters for
biochemical reactions can facilitate deeper insights into the workings and the design of …
biochemical reactions can facilitate deeper insights into the workings and the design of …