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Popular tool citations

chevron_left Circular dichroism spectroscopy analysis Circular dichroism spectroscopy simulation chevron_right
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DichroCalc specifications

Information


Unique identifier OMICS_12756
Name DichroCalc
Interface Web user interface
Restrictions to use None
Input format .pdb, .tar, .tar.gz, .gz, .tgz, .zip, .Z
Programming languages Fortran, Perl
Computer skills Basic
Version 3.3
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Jonathan D. Hirst

Publication for DichroCalc

DichroCalc citations

 (5)
library_books

Genetic identification and molecular modeling characterization reveal a novel PROM1 mutation in Stargardt4 like macular dystrophy

2017
Oncotarget
PMCID: 5787432
PMID: 29416601
DOI: 10.18632/oncotarget.22343

[…] the wild type and l245p mutant over the whole simulation period., the secondary structure of the wild-type and p.l245p mutant system were determined by cd spectroscopy during 130 ns modeling using dichrocalc server []. cd spectroscopy is a well-established technique for measuring the secondary structure, dynamics, and folding pathways of proteins in the “far-uv” spectral region (190-250 nm); […]

library_books

Computing infrared spectra of proteins using the exciton model

2016
J Comput Chem
PMCID: 5434914
PMID: 27868210
DOI: 10.1002/jcc.24674

[…] of force constants calculated ab initio for all combinations of main‐chain dihedral angles (in increments of 30°) for a di‐peptide., we now turn to the calculation (using a modified version of the dichrocalc software) of the diagonal elements of the hamiltonian and the change in frequency for each local mode due to the surrounding electrostatic environment. the electrostatic potential at site […]

library_books

Action FRET of a Gaseous Protein

2016
J Am Soc Mass Spectrom
PMCID: 5174150
PMID: 27506208
DOI: 10.1007/s13361-016-1449-2

[…] ch3oh, each with 1% acetic acid by volume, supplementary figure sa. predicted circular dichroism for native (1 ubq), partially and fully unfolded species described above were calculated using the dichrocalc web-interface [], shown in supplementary figure sb. analysis of secondary structure elements reveals that the partially unfolded structure appears to possess a significant disordered […]

library_books

Structural Insight of Dopamine β Hydroxylase, a Drug Target for Complex Traits, and Functional Significance of Exonic Single Nucleotide Polymorphisms

2011
PLoS One
PMCID: 3197665
PMID: 22028891
DOI: 10.1371/journal.pone.0026509

[…] web servers, 3v server available at http://3vee.molmovdb.org/index.php with 1.4 å probe radius and vadar available at http://vadar.wishartlab.com/ .cd spectrum for the model was calculated using dichrocalc available at http://comp.chem.nottingham.ac.uk/dichrocalc/ ., subsequent to model building, the quaternary structure of the enzyme was also obtained in silico. it is known that the soluble […]

library_books

Structural and Functional Characterization of Human Peripheral Nervous System Myelin Protein P2

2010
PLoS One
PMCID: 2858655
PMID: 20421974
DOI: 10.1371/journal.pone.0010300

[…] of high-beta folds is a commonly known caveat of cd spectrum deconvolution algorithms. the results do show that recombinant human p2 is folded, as expected, into a mainly β-sheet structure., dichrocalc was used to calculate theoretical cd spectra from the experimental atomic coordinates. the srcd spectrum of human recombinant p2 was then compared with the back-calculated spectrum (). […]


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DichroCalc institution(s)
School of Chemistry, University of Nottingham, Nottingham, UK
DichroCalc funding source(s)
EPSRC (grant number GR/T09224)

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