References

Publications referring to DichroWeb :


Whitmore, L. and Wallace, B.A. (2008) Protein Secondary Structure Analyses from Circular Dichroism Spectroscopy: Methods and Reference Databases. Biopolymers 89, 392-400. (PDF)

Whitmore, L. and Wallace, B.A. (2004) DICHROWEB: an online server for protein secondary structure analyses from circular dichroism spectroscopic data. Nucleic Acids Research 32:W668-673 (PDF)

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.


DichroWeb includes using the following 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.

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.

CONTINLL

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

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.

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.

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.

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.

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.

Protein Reference Data Sets

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.

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

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.

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.

NRMSD Parameter

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