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Protocols

Cofactory specifications

Information


Unique identifier OMICS_16373
Name Cofactory
Interface Web user interface
Restrictions to use None
Input data The protein sequence.
Input format FASTA
Output data The protein features.
Output format Textual format
License Other
Computer skills Basic
Version 1.0
Stability Stable
Source code URL http://www.cbs.dtu.dk/services/doc/cofactory-1.0.readme
Maintained Yes

Documentation


Maintainer


  • person_outline Thomas Nordahl Petersen <>

Information


Unique identifier OMICS_16373
Name Cofactory
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data The protein sequence.
Input format FASTA
Output data The protein features.
Output format Textual format
Operating system Unix/Linux
License Other
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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No version available

Documentation


Maintainer


  • person_outline Thomas Nordahl Petersen <>

Publication for Cofactory

Cofactory citations

 (4)
library_books

Exploring complex cellular phenotypes and model guided strain design with a novel genome scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome

2016
PMCID: 5012057
PMID: 27602057
DOI: 10.1186/s13068-016-0607-x

[…] recently expanded knowledge of c. thermocellum metabolism. in particular, we updated the cofactor specificity of glycolytic enzymes [] based on in vitro protein characterization as well as performed cofactory analysis [] to resolve cofactor specificity when in vitro data was unavailable (see “” section). we also manually curated the intricate carbon overflow and redox metabolisms with recently […]

library_books

A sacrificial millipede altruistically protects its swarm using a drone blood enzyme, mandelonitrile oxidase

2016
PMCID: 4893617
PMID: 27265180
DOI: 10.1038/srep26998

[…] clones to avoid pcr-derived sequence errors, and the dna and amino acid sequences of chuamox were analyzed using genetyx ver. 11 and atgc (genetyx, tokyo, japan), peptidemass, netnglyc 1.0 server, cofactory, and mega6., each experimental tissue was collected as described above and immediately homogenized in a trizol reagent (thermo fisher scientific) after the addition of glycogen (thermo […]

call_split

Substitutions at the cofactor phosphate binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity

2015
PMCID: 4498498
PMID: 26034298
DOI: 10.1093/protein/gzv028
call_split See protocol

[…] on a specific family of enzymes, rather than an entire class or all those with a shared fold, is a more successful strategy for developing rules to switch cofactors., a recently described algorithm, cofactory (), uses primary sequence information to predict the cofactor-binding specificities of rossmann folds. when we retrospectively entered the caadh sequence into this webserver, it could […]

library_books

Prevalence and correlates of vitamin K deficiency in children with inflammatory bowel disease

2014
PMCID: 3998013
PMID: 24759680
DOI: 10.1038/srep04768

[…] may lead to vitamin k sufficiency in different patients. thus, the estimation of vitamin k status using pivka-ii concentrations may present an advantage in that it reflects a lack of vitamin k cofactory function enabling for carboxylation of vitamin k-dependent compounds. however, there are factors other than vitamin k status that influence pivka-ii concentration and it cannot be ruled […]


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Cofactory funding source(s)
This work was supported by Novo Nordisk Foundation and Novozymes A/S.

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