References

DichroWeb Publications


Miles, A.J, Ramalli, S.G, and Wallace, B.A. (2021) DichroWeb, a website for calculating protein secondary structure from circular dichroism spectroscopic data. Protein Science: https://doi.org/10.1002/pro.4153
Pubmed

Whitmore, L. and Wallace, B.A. (2008) Protein secondary structure analyses from circular dichroism spectroscopy: Methods and Reference Databases. Biopolymers 89: 392-400.
Pubmed

Whitmore, L. and Wallace, B.A. (2004) DICHROWEB: an online server for protein secondary structure analyses from circular dichroism spectroscopic data. Nucleic Acids Res 32: W668 - 73.
Pubmed

Lobley, A., Whitmore, L. and Wallace, B.A. (2002) DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra. Bioinformatics 18: 211-212.
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Algorithms


SELCON3

Sreerema, N. and Woody, R.W. (1993) A self-consistent method for the analysis of protein secondary structure from circular dichroism. Anal. Biochem. 209: 32-44.
Pubmed

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.
Pubmed

CONTINLL

Provencher, S.W. and Glockner, J. (1981) Estimation of globular protein secondary structure from circular dichroism. Biochemistry 20: 33-37.
Pubmed

Van Stokkum, I.H.M., Spoelder, H.J.W., Bloemendal, M., Van Grondelle, R., and Groen, F.C.A. (1990) Estimation of protein secondary structure and error analysis from CD spectra. Anal. Biochem. 191: 110-118.
Pubmed

VARSLC & CDSSTR

Compton, L.A. and Johnson, W.C., Jr. (1986) Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication. Anal. Biochem. 155: 155-167.
Pubmed

Manavalan, P. and Johnson, W.C., Jr. (1987) Variable selection method improves the prediction of protein secondary structure from circular dichroism spectra. Anal. Biochem. 167: 76-85.
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Sreerama, N. and Woody, R.W. (2000) Estimation of protein secondary structure from CD spectra: Comparison of CONTIN, SELCON and CDSSTR methods with an expanded reference set. Anal. Biochem. 287(2): 252-260.
Pubmed

K2D

Andrade, M.A., Chacón, P., Merelo, J.J. and Morán, F. (1993) Evaluation of secondary structure of proteins from UV circular dichroism using an unsupervised learning neural network. Prot. Engineering 6: 383-390.
Pubmed


Protein Reference Data Sets


Sets 1-7

Sreerama, N. and Woody, R.W. (2000) Estimation of protein secondary structure from CD spectra: Comparison of CONTIN, SELCON and CDSSTR methods with an expanded reference set. Anal. Biochem. 287(2): 252-260.
Pubmed

Sreerama, N., Venyaminov, S.Y. and Woody, R.W. (2000) Estimation of protein secondary structure from CD spectra: Inclusion of denatured proteins with native protein in the analysis. Anal. Biochem. 287: 243-251.
Pubmed

SP175

Lees, J.G., Miles, A.J., Wien, F., and Wallace, B.A. (2006) A reference database for circular dichroism spectroscopy covering fold and secondary structure space. Bioinformatics 22: 1955-1962.
Pubmed

SMP180

Abdul-Gader, A., Miles, A.J., Wallace, B.A. (2011) A reference dataset for the analyses of membrane protein secondary structures and transmembrane residues using circular dichroism spectroscopy. Bioinformatics 27: 1630-1636.
Pubmed

Cryst175

Evans, P., Bateman, O.A., Slingsby, C., and Wallace, B.A. (2007) A reference dataset for circular dichroism spectroscopy tailored for the beta-gamma-crystallin lens proteins. Experimental Eye Res. 84: 1001-1008.
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Background Publications


Miles AJ, Janes RW, Wallace BA (2021) Tools and methods for circular dichroism spectroscopy of proteins. Chem Soc Rev, in press.

Miles AJ, Wallace BA (2016) Circular dichroism spectroscopy of membrane proteins. Chem Soc Rev 45: 4859-4872.
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Miles AJ, Wallace BA (2006) Synchrotron radiation circular dichroism spectroscopy of proteins and applications in structural and functional genomics. Chem Soc Rev 35: 39-51.
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NRMSD Parameter

Mao, D., Wachter, E. and Wallace, B.A. (1982) Folding of the H+-ATPase Proteolipid in Phospholipid Vesicles. Biochemistry, 21: 4960-4968.
Pubmed

Scaling

Miles AJ, Whitmore L, Wallace BA (2005) Spectral magnitude effects on the analyses of secondary structure from circular dichroism spectroscopic data. Prot Sci, 14: 368-374.
Pubmed