Bioinformatics Advance Access originally published online on June 20, 2006
Bioinformatics 2006 22(16):1955-1962; doi:10.1093/bioinformatics/btl327
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
A reference database for circular dichroism spectroscopy covering fold and secondary structure space
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1 Department of Crystallography, Birkbeck College, University of London London WC1E 7HX, UK
2 Centre for Protein and Membrane Structure and Dynamics, Daresbury Laboratory Warrington WA4 4AD, UK
*To whom correspondence should be addressed (at Birkbeck).
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Abstract |
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Motivation: Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined.
This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology.
Contact: b.wallace{at}mail.cryst.bbk.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
|Current address: School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS UK
~Current address: Synchrotron Soleil, Orme Merisiers, BP 48 St. Aubin, Gif sur Yvette, F-91192 France
These authors contributed equally to this work
Associate Editor: Alex Bateman
Received on April 11, 2006; revised on June 7, 2006; accepted on June 8, 2006
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