K2D protocols

View K2D computational protocol

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chevron_left Secondary structure prediction Circular dichroism spectroscopy analysis chevron_right
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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 in pipeline

2011
PMCID: 3107778
PMID: 21554724
DOI: 10.1186/1471-2180-11-95

[…] dichroism spectrum (figure ), which showed a typical signature of an alpha helical protein. the percentage of helical structure of yqic, estimated through the analysis of its cd spectra using k2d program (63%), agrees with the percentage of amino acids involved in the predicted n- and c-terminal alpha helices., on the other hand, we studied the oligomeric state of yqic by chemical […]


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K2D in publications

 (24)
PMCID: 5859067
PMID: 29555908
DOI: 10.1038/s41598-018-22744-5

[…] 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 […]

PMCID: 5748837
PMID: 29150435
DOI: 10.1042/BCJ20170351

[…] 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, […]

PMCID: 5529560
PMID: 28747797
DOI: 10.1038/s41598-017-06653-7

[…] the molecular mass of recombinant pmvrp15 was 15,899.9 da (data not shown), which corresponded to the calculated mw of pmvrp15 protein (15,859.5 da), using expasy server. cd spectra were analysed by k2d, continll and cdsstr algorithms via dichroweb, using a mixed soluble and membrane protein dataset, smp180, as reference. cdsstr produced the best fit to the experimental data (nrmsd = 0.001), […]

PMCID: 5357790
PMID: 28317901
DOI: 10.1038/srep44695

[…] using 1mm path length glass cuvettes (starna scientific, essex, uk) at 25 °c. respective blank measurements were subtracted from all samples and the percentage of α-helix was calculated using k2d3 at http://k2d3.ogic.ca/., m2ah structures were examined using a 500 μm solution of the 16aa a/udorn/72 m2ah domain in 90% h2o/10% d2o with 10 μm popc:popg:cholesterol luvs, where indicated. […]

PMCID: 5632712
PMID: 29114584
DOI: 10.1016/j.bbrep.2016.12.006

[…] the helical contents of hbx(101−136)-(gs)5-bcl-xl and bcl-xl were estimated using the average of two experiments by the chen and yang method , the helix-coil model method , , and the program k2d3 . in the chen and yang method, the following equation was used:(1)helicalcontent(%)=−([θ’]222+2,340)/30,300×100where [θ’]222 is the mean residue molar ellipticity [θ’] at 222 nm., […]


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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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