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Protocols

K2D specifications

Information


Unique identifier OMICS_12755
Name K2D
Interface Web user interface
Restrictions to use None
Input data A CD spectrum of a protein.
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Carol Perez-Iratxeta

Publications for K2D

K2D citations

 (93)
library_books

Analysis of β tubulin carbendazim interaction reveals that binding site for MBC fungicides does not include residues involved in fungicide resistance

2018
Sci Rep
PMCID: 5940828
PMID: 29740047
DOI: 10.1038/s41598-018-25336-5

[…] ponse time of 1 s, using a 0.3-cm path-length cuvette. The results were expressed as mean residue ellipticity as described elsewhere. Secondary structure estimation from CD spectra was obtained using K2D software (www.ogic.ca/projects/k2d3/). […]

library_books

High yield bacterial expression, purification and characterisation of bioactive Human Tousled like Kinase 1B involved in cancer

2018
Sci Rep
PMCID: 5859067
PMID: 29555908
DOI: 10.1038/s41598-018-22744-5

[…] re prediction server and predicted to be 19 and 14 respectively (PSIPRED analysis, Supplementary Figure, S). The total percentage of alpha helices and beta sheets were also calculated in-silico using K2D3 software and were found to be 29.5% and 17.4% (Fig. ). We found that 0.3 mg/ml concentration of the protein estimated by absorbance spectroscopy at 280 nm using calculated extinction coefficient […]

library_books

Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1

2018
Sci Rep
PMCID: 5832771
PMID: 29497085
DOI: 10.1038/s41598-018-21952-3

[…] l quartz cuvette (Hellma). Each spectrum represents an average of 10 continuous scans (100 nm min−1) with response time 0.25 s and bandwidth 1.0 nm. CD spectra of the peptides were analysed using the K2D2 web server (Supplementary Fig. ). Secondary structure content of the protein constructs was calculated in programs CDSSTR, CONTIN and SELCON3, from CDPro software package using the reference prot […]

library_books

Hydroxynitrile lyases from cyanogenic millipedes: molecular cloning, heterologous expression, and whole cell biocatalysis for the production of (R) mandelonitrile

2018
Sci Rep
PMCID: 5813103
PMID: 29445093
DOI: 10.1038/s41598-018-20190-x

[…]  nm; bandwidth, 2.0 nm; sensitivity, 100 mdeg; response, 1 s; speed, 100 nm.min−1; and accumulation, 10–20. Every sample was measured in triplicate and data were analyzed using the DichroWeb with the K2D method. […]

library_books

Biochemical characterization of INTS3 and C9ORF80, two subunits of hNABP1/2 heterotrimeric complex in nucleic acid binding

2018
PMCID: 5748837
PMID: 29150435
DOI: 10.1042/BCJ20170351

[…] CD spectroscopy (), where the protein exhibited a minimal ellipticity, negative bands near 200 nm corresponding to random coil conformation, and a dip at 208 nm suggesting α-helix. When analyzed with K2d method [] using the DichroWeb software [], 48% of the protein exhibits random coil, 37% corresponds for α-helix, and 15% with β-sheets, which is close to the results predicted. Therefore, we concl […]

call_split

Biophysical and functional characterization of the N terminal domain of the cat T1R1 umami taste receptor expressed in Escherichia coli

2017
PLoS One
PMCID: 5662223
PMID: 29084235
DOI: 10.1371/journal.pone.0187051
call_split See protocol

[…] -nm/min scan speed and 5-s response times. They were smoothed using the Stavitzky-Golay convolution filter with a span of 5. The secondary structure proportions were estimated using the deconvolution K2D algorithm on DichroWeb program (http://dichroweb.cryst.bbk.ac.uk/html/home.shtml) []. […]

Citations

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K2D institution(s)
Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada; Max Delbrück Center for Molecular Medicine, Berlin, Germany

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