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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.
Pubmed
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.
Pubmed
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.
Pubmed
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.
Pubmed
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.
Pubmed
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