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Number of citations per year for the bioinformatics software tool eQuilibrator
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Protocols

eQuilibrator specifications

Information


Unique identifier OMICS_06492
Name eQuilibrator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability No
Maintained No

Versioning


No version available

Information


Unique identifier OMICS_06492
Name eQuilibrator
Interface Web user interface
Restrictions to use None
Programming languages Javascript, Python
Computer skills Basic
Stability No
Maintained No

Publication for eQuilibrator

eQuilibrator citations

 (14)
call_split

In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host

2017
Front Microbiol
PMCID: 5727896
PMID: 29276507
DOI: 10.3389/fmicb.2017.02440
call_split See protocol

[…] ns.” This is a fast algorithm, but is limited by the completeness and accuracy of the input metabolic network and database.Since reaction downloads from KEGG do not contain reversibility information, eQuilibrator () was used to computationally estimate the reversibility of every KEGG reaction. FGF was applied individually to the mouse cytosol and the Bt cell to fill the gaps in both the biosynthet […]

library_books

Renewable synthesis of n butyraldehyde from glucose by engineered Escherichia coli

2017
Biotechnol Biofuels
PMCID: 5713646
PMID: 29213330
DOI: 10.1186/s13068-017-0978-7

[…] carbon flux was reduced. Analysis of the thermodynamics of each step revealed that butyryl-CoA reduction to n-butyraldehyde is thermodynamically unfavorable with ΔG′° of 7.7 kJ/mol (calculated using eQuilibrator []), which may lead to inefficient conversion of butyryl-CoA to n-butyraldehyde, particularly after n-butyraldehyde concentration reached a certain threshold. It is likely that as n-butyr […]

library_books

A review of computational tools for design and reconstruction of metabolic pathways

2017
PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] ted based on their most negative overall ΔG, which sums up the ΔG of each reaction step. Group Contribution Method , and a recently developed and publicly available Component Contributions Method or eQuilibrator can be used to estimate the standard transformed Gibbs free energy of reaction under the host cell environment (e.g., cellular compartment pH, growth temperature). Knowledge of the intra […]

library_books

Quantifying pCO2 in biological ocean acidification experiments: A comparison of four methods

2017
PLoS One
PMCID: 5619781
PMID: 28957378
DOI: 10.1371/journal.pone.0185469

[…] with AT as the second carbonate chemistry parameter, all four methods produced very similar pCO2 estimates, and the three field methods 1) spectrophotometric pHT, 2) electrode pHNBS, and 3) NDIR CO2 equilibrator, performed comparably to CT with careful use. In this study, electrode pHNBS and the CO2 equilibrator gave consistently close results to CT-derived pCO2 values, and had the smallest range […]

library_books

Heritability of behavioural tolerance to high CO 2 in a coral reef fish is masked by nonadaptive phenotypic plasticity

2017
Evol Appl
PMCID: 5511360
PMID: 28717388
DOI: 10.1111/eva.12483

[…] eau of Standards) and temperature measurements were taken in each tank using a pH electrode (SevenGo Pro, Mettler Toledo, Switzerland) and temperature probe (Cormark C26, Norfolk, UK). A portable CO2 equilibrator and infrared sensor (GMP343, Vaisala, Helsinki, Finland) verified seawater pCO2 (Hari et al., ; Munday, Watson, Chung, Marshall, & Nilsson, ). Water samples were taken for the duration of […]

library_books

How important is thermodynamics for identifying elementary flux modes?

2017
PLoS One
PMCID: 5319754
PMID: 28222104
DOI: 10.1371/journal.pone.0171440

[…] t available. In contrast, the equilibrium constants are relatively easy to obtain because they are independent of the properties of the enzymes. These constants can be found in a very useful database eQuilibrator [] which used methods developed by Noor et al. [, ] based on thermochemical estimation. Moreover, several approaches have been published for computing equilibrium constants (or the equiva […]


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eQuilibrator institution(s)
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel

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