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|Interface||Web user interface|
|Restrictions to use||None|
|Input format||.pdb, .tar, .tar.gz, .gz, .tgz, .zip, .Z|
|Programming languages||Fortran, Perl|
- Documentation: http://comp.chem.nottingham.ac.uk/dichrocalc/help.html
- person_outline Jonathan D. Hirst
Publication for DichroCalc
Genetic identification and molecular modeling characterization reveal a novel PROM1 mutation in Stargardt4 like macular dystrophy
[…] 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 […]
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.
[…] 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 […]
Computing infrared spectra of proteins using the exciton model
[…] 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 […]
Action FRET of a Gaseous Protein
[…] 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 […]
Conformational Effects on the Circular Dichroism of Human Carbonic Anhydrase II: A Multilevel Computational Study
[…] 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 […]
Structural Insight of Dopamine β Hydroxylase, a Drug Target for Complex Traits, and Functional Significance of Exonic Single Nucleotide Polymorphisms
[…] 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/ . […]
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