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Bioinformatics Advance Access originally published online on January 7, 2009
Bioinformatics 2009 25(4):539-540; doi:10.1093/bioinformatics/btp016
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

DichroCalc—circular and linear dichroism online

Benjamin M. Bulheller 1 and Jonathan D. Hirst 1,*

1School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK

*To whom correspondence should be addressed.


  Abstract

Motivation: Circular dichroism (CD) is widely used in studies of protein folding. The CD spectrum of a protein can be estimated from its structure alone, using the well-established matrix method. In the last decade, a related spectroscopy, linear dichroism (LD), has been increasingly applied to study the orientation of proteins in solution. However, matrix method calculations of LD spectra have not been presented before. DichroCalc makes both CD and LD calculations available in an easy-to-use fashion.

Results: DichroCalc can be used without registration and calculates CD and LD spectra using a variety of matrix method parameters. PDB files can be uploaded as input or retrieved via their PDB code and a Perl-based parser is offered for easy handling of PDB files.

Availability: http://comp.chem.nottingham.ac.uk/dichrocalc and http://comp.chem.nottingham.ac.uk/parsepdb

Contact: jonathan.hirst{at}nottingham.ac.uk

Associate Editor: Anna Tramontano

Received on October 27, 2008; revised on December 12, 2008; accepted on January 5, 2009

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