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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

 (7)
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 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); wh […]

library_books

Quantitative first principles calculations of protein circular dichroism in the near ultraviolet† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00586e Click here for additional data file. Click here for additional data file.

2017
PMCID: 5637123
PMID: 29163925
DOI: 10.1039/c7sc00586e

[…] e size and the complexity of proteins, it is impractical to obtain the wave functions from ab initio calculations. Instead, we calculate protein CD spectra using the matrix method,, as implemented in DichroCalc code. In the matrix method, the proteins are considered as being composed of M chromophores. The wave function of the protein in its k th excited state, ψ k, is expressed as a linear combin […]

library_books

Computing infrared spectra of proteins using the exciton model

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

[…] ists 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 i […]

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

[…] and 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 charac […]

library_books

Conformational Effects on the Circular Dichroism of Human Carbonic Anhydrase II: A Multilevel Computational Study

2013
PLoS One
PMCID: 3582176
PMID: 23526922
DOI: 10.1371/journal.pone.0056874

[…] ere taken from MD simulations.The CD calculations with the matrix method were performed incorporating all peptides and side chain chromophores. The matrix method calculations were performed using the Dichrocalc web interface . This method in its origin-independent form considers the protein as a system of M independent chromophoric groups. The wave function of the entire molecule is represented […]

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

[…] ent 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/ . […]

Citations

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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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