Welcome to DichroCalc, our web interface for protein circular and linear dichroism calculations.

Link to the C++ version of DichroCalc on GitHub.

You can upload .pdb files, experimental spectra and archives containing several files. File types that can be handled by DichroCalc:

• .pdb
• .tar, .tar.gz, .gz, .tgz
• .zip
• .Z

Instead of uploading a file, you can also (or additionally) enter one or more PDB codes of proteins which are then downloaded from the RCSB Protein Data Bank. If you enter more than one code, please separate them by spaces.

If you want to run calculations on non-standard residues, simply make sure that the atoms in the .pdb file are labelled with the ATOM-keyword and the peptide chain is denoted by C, N, O, CA labels.

The calculated spectra are provided as text files containing the xy-data and are also plotted as postscript file. If you additionally provide the experimental data, a comparison plot is created. To use this feature, add the experimental spectrum with the extension .exp.cd or .exp.ld to the archive containing the pdb file (i.e. 1beb.pdb and 1beb.exp.cd).

The supported chromophores for CD and LD calculations are:

• peptide bonds (and charge-transfer between adjacent peptide bonds);
• the aromatic side chain chromophores of phenylalanine, tyrosine, and tryptophan (accounting for the vibrational structure of the electronic transitions);
• the side chain chromophores of asparagine, aspartic acid, glutamine, and gluamic acid;
• the nucleic bases adenine, guanine, cytosine, thymine and uracil for RNA and DNA calculations;
• the naphthalenediimide chromophore.

For additional information on the interface, please have a look at the help section.

Jonathan Hirst

Originally funded by

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