A reference database for circular dichroism spectroscopy covering fold and secondary structure space
By Jonathan G. Lees, A. Miles, Frank Wien, B. Wallace. Bioinform., 2006
425 citations recorded by the source corpus.
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.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/d6ce8493f4674983623c5a6bed49050bffe3913f
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Citations in the corpus
- Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy: New beamlines and new applications in biology (2007, positive): “SRCD spectrum of horse myoglobin obtained on beamline 4B8 (black line) overlaid on the myoglobin spectrum in the SP175 reference dataset (grey line) [9].”
- BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra (2018, positive): “The reference set consisted of the spectra of the SP175 SRCD reference set of PCDDB (15) and some additional - structure-rich spectra that were also deposited in PCDDB (see Micsonai et al (11)).”