PMID- 16787970
OWN - NLM
STAT- MEDLINE
DCOM- 20060928
LR  - 20130520
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Linking)
VI  - 22
IP  - 16
DP  - 2006 Aug 15
TI  - A reference database for circular dichroism spectroscopy covering fold and
      secondary structure space.
PG  - 1955-62
AB  - 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.
FAU - Lees, Jonathan G
AU  - Lees JG
AD  - Department of Crystallography, Birkbeck College, University of London, London
      WC1E 7HX, UK.
FAU - Miles, Andrew J
AU  - Miles AJ
FAU - Wien, Frank
AU  - Wien F
FAU - Wallace, B A
AU  - Wallace BA
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20060620
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
SB  - IM
MH  - Algorithms
MH  - Biophysics/methods
MH  - Calibration
MH  - Circular Dichroism/*methods
MH  - Cluster Analysis
MH  - Computational Biology/methods
MH  - Databases, Genetic
MH  - *Databases, Protein
MH  - Protein Folding
MH  - Protein Structure, Secondary
MH  - Ultraviolet Rays
EDAT- 2006/06/22 09:00
MHDA- 2006/09/29 09:00
CRDT- 2006/06/22 09:00
PHST- 2006/06/22 09:00 [pubmed]
PHST- 2006/09/29 09:00 [medline]
PHST- 2006/06/22 09:00 [entrez]
AID - btl327 [pii]
AID - 10.1093/bioinformatics/btl327 [doi]
PST - ppublish
SO  - Bioinformatics. 2006 Aug 15;22(16):1955-62. doi: 10.1093/bioinformatics/btl327.
      Epub 2006 Jun 20.