User guide

Reference Proteins

Table 1: Reference Sets 1-7 and SP175

This table details the reference proteins which are in each reference data set. For additional information see:

Janes, R.W. (2008) Reference Datasets Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy of Proteins. in: Modern Techniques in Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy (Wallace, B.A. and Janes, R.W., eds). IOS Press, 2009. ISBN-10: 1607500000

Citation details for the reference sets can be found in the references section.

Name Set 1 Set 2 Set 3 Set 4 Set 5 Set 6 Set 7 SP175‡
Range (nm) 178-260 178-260 185-240 190-240 178-260 185-240 190-240 175-260
Key
 αR αD βR βD T U α 3/10 β T P2 U αR αD βR βD T U αR αD βR βD T U α β T P2 U αR αD βR βD T U αR αD βR βD T U αR αD βR βD T U
AAMY reference set contains this protein
ABNG reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein†
ACY5 reference set contains this protein reference set contains this protein
ACY9 reference set contains this protein reference set contains this protein
ADH reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
ADK reference set contains this protein reference set contains this protein
ALDO reference set contains this protein
APP reference set contains this protein
APRT reference set contains this protein
AVDN reference set contains this protein
AZU reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
BAMY reference set contains this protein
BB2C reference set contains this protein
BGAL reference set contains this protein
BLAC reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein†
BNJN reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
BPTI reference set contains this protein reference set contains this protein
CA1 reference set contains this protein
CANH reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
CAL reference set contains this protein
CAT reference set contains this protein
CER reference set contains this protein
CGA reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
CHYT reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
CITS reference set contains this protein
ColA reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
CONA reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein†
CPAS reference set contains this protein reference set contains this protein reference set contains this protein
CPHY reference set contains this protein
CYTC reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein†
DHQ1 reference set contains this protein
DHQ2 reference set contains this protein
DNA1 reference set contains this protein
ECOR reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
ELAS reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
FERD reference set contains this protein
FLVD reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
GCR reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
GDCH reference set contains this protein
GDCB reference set contains this protein
GEC reference set contains this protein
GFP reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
GLOX reference set contains this protein
GLUD reference set contains this protein
GPB reference set contains this protein
GPD reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
GRS reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
GSCR reference set contains this protein
HAL reference set contains this protein
HBN reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein†
HGDC reference set contains this protein
HMRT reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
HSA reference set contains this protein
IFBP reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
IGG reference set contains this protein
INSL reference set contains this protein reference set contains this protein reference set contains this protein†
JAC reference set contains this protein
LACF reference set contains this protein
LDH reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
LEP reference set contains this protein
LLEC reference set contains this protein
LYSM reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein†
MBH reference set contains this protein
MGLB reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein†
MON reference set contains this protein
NMRA reference set contains this protein
NUCL reference set contains this protein reference set contains this protein
OVAL reference set contains this protein
OVOT reference set contains this protein
OX20 reference set contains this protein reference set contains this protein
PAPN reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein†
PARV reference set contains this protein reference set contains this protein
PELC reference set contains this protein
PGK reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
PGLU reference set contains this protein
PGM reference set contains this protein
PLA2 reference set contains this protein
PLEC reference set contains this protein
PNMT reference set contains this protein
PPSN reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
PRAL reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
PROX reference set contains this protein
PYK reference set contains this protein
RHD reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein†
RNAS reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
RUBR reference set contains this protein reference set contains this protein
SN06 reference set contains this protein reference set contains this protein
SN70 reference set contains this protein reference set contains this protein
STI reference set contains this protein
STRP reference set contains this protein
SUBA reference set contains this protein
SUBB reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
SUBN reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
SUDS reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein†
THAU reference set contains this protein
T4LS reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
THML reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
TNF reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein
TPI reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein reference set contains this protein†
TRPN reference set contains this protein
UBIQ reference set contains this protein
† denotes that the source for this protein has the same name but a different PDB code from that used for Sets 1-7
‡ All reference spectra for SP175 were recorded using a synchrotron light source

Table 2: Reference Set CRYST175

Name : CRYST175Range (nm) : 175-260 Classifications: αR αD βR βD T U
BGB bovine gamma B crystallin BGD bovine gamma D crystallin
BGE bovine gamma E crystallin E11 bovine gamma crystallin E11 mutant
HBB2 human beta B2 crystallin HGSC human gamma S crystallin (C-terminal domain)
HGD human gamma D crystallin HBB1 human beta B1 crystallin
HBBT human beta B1 crystallin (truncated)
Evans, P., Bateman, O.A., Slingsby, C., and Wallace, B.A. (2007) A Reference Dataset for Circular Dichroism Spectroscopy Tailored for the βB2-Crystallin Lens Proteins. Experimental Eye Research 84 1001-1008.

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Table 3: Reference Set SMP180

Name : SMP180Range (nm) : 180-240 Classifications: αR αD βR βD T U
SMP180 includes all the proteins of SP175 plus the proteins which have these PDB codes:
1qhj 1kpk 2cfq 2nu9 2nop 1hzx
1l7v 1rh5 2dyr 1j95 2oar 2gif
1pcr 2wjn 1be3 1t5s 1nek 1xl4
2j58 3jqo 1uyn 1a0s 1fcp 1fep
1nqh 2vdf 2iwv 1h2s 2a65 1nkz
1hml 1gai 2hav 1t4b 2j0x 1azu
2rhe 2rhe 1k9b 1xag 5dfr 2nwe
1ies 2j41 1a8e 1xag 1wnh 2ox0
1bn8 2pab 1kit 1hk9 1jpc 2sns
2j51 1sfl 9wga 2gel
A Reference Dataset for the Analyses of Membrane Protein Secondary Structures and Transmembrane Residues using Circular Dichroism Spectroscopy. Ali Abdul-Gader, Andrew John Miles and B.A. Wallace (2011) Bioinformatics 27 1630-6.

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Secondary Structure Classifications

For the algorithms that accept selectable reference sets, the output that they give is defined by the secondary structure classifications of the reference data. Selection of a reference set is thus made by a consideration of what type of secondary structure definitions are desired and the range of data that is available (310 and Polyproline II helix can only be analysed for with larger wavelength ranges).

The majority of output is given in terms of a 6 classification output devised by Woody and co-workers. For a full description of the classifications see:

Sreerema, N., Venyaminov, S.Y., and Woody, R.W. (1999) Estimation of the number of helical and strand segments in proteins using CD spectroscopy. Protein Sci. 8, 370-380.
αRAlpha helix, regular (helix 1)
αDAlpha helix, distorted (helix 2)
βRBeta sheet, regular (sheet 1)
βDBeta sheet, distorted (sheet 2)
TTurns
UUnordered

Reference Sets 2 and 5 have different secondary structure definitions and may be used to analyse for 310 helix (SET 2 only) and polyproline II helix. Sets 2 and 5 require data to cover the range 178-260nm.
αAlpha helix
βBeta sheet
3/10310 helix (SET 2 only)
P2Polyproline II helix
TTurns
UUnordered

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