PMID- 21505036
OWN - NLM
STAT- MEDLINE
DCOM- 20110920
LR  - 20181201
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Linking)
VI  - 27
IP  - 12
DP  - 2011 Jun 15
TI  - A reference dataset for the analyses of membrane protein secondary structures and
      transmembrane residues using circular dichroism spectroscopy.
PG  - 1630-6
LID - 10.1093/bioinformatics/btr234 [doi]
AB  - MOTIVATION: Empirical analyses of protein secondary structures based on circular 
      dichroism (CD) and synchrotron radiation circular dichroism (SRCD) spectroscopic 
      data rely on the availability of reference datasets comprised of spectra of
      relevant proteins, whose crystal structures have been determined. Datasets
      comprised of only soluble proteins have not proven suitable for analysing the
      spectra of membrane proteins. RESULTS: A new reference dataset, MP180, has been
      created containing the spectra of 30 membrane proteins encompassing the secondary
      structure and fold space covered by all known membrane protein structures. In
      addition a mixed soluble and membrane protein dataset, SMP180, has been created, 
      which includes 98 soluble protein spectra (SP) plus the MP180 spectra.
      Calculations of both membrane and soluble protein secondary structures using
      SMP180 are significantly improved with respect to those produced, using soluble
      protein-only datasets. The SMP180 dataset also enables determination of the
      percentage of transmembrane residues, thus enhancing the information previously
      obtainable from CD spectroscopy. AVAILABILITY AND IMPLEMENTATION: Reference
      dataset online at the DichroWeb analysis server
      (http://dichroweb.cryst.bbk.ac.uk); individual protein spectra in the Protein
      Circular Dichroism Data Bank (http://pcddb.cryst.bbk.ac.uk).
FAU - Abdul-Gader, Ali
AU  - Abdul-Gader A
AD  - Department of Crystallography, Institute of Structural and Molecular Biology,
      Birkbeck College, University of London, London WC1E 7HX, UK.
FAU - Miles, Andrew John
AU  - Miles AJ
FAU - Wallace, B A
AU  - Wallace BA
LA  - eng
GR  - BB/D008581/1/Biotechnology and Biological Sciences Research Council/United
      Kingdom
GR  - Biotechnology and Biological Sciences Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20110419
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
RN  - 0 (Membrane Proteins)
SB  - IM
MH  - *Circular Dichroism/methods
MH  - *Databases, Protein
MH  - Membrane Proteins/*chemistry
MH  - Protein Structure, Secondary
MH  - Synchrotrons
EDAT- 2011/04/21 06:00
MHDA- 2011/09/21 06:00
CRDT- 2011/04/21 06:00
PHST- 2011/04/21 06:00 [entrez]
PHST- 2011/04/21 06:00 [pubmed]
PHST- 2011/09/21 06:00 [medline]
AID - btr234 [pii]
AID - 10.1093/bioinformatics/btr234 [doi]
PST - ppublish
SO  - Bioinformatics. 2011 Jun 15;27(12):1630-6. doi: 10.1093/bioinformatics/btr234.
      Epub 2011 Apr 19.