Useful links

Projects related to DichroWeb
 

Neural Network Servers
 

Software Methods References
 

References
 

Projects related to DichroWeb ...
 

The Protein Circular Dichroism DataBank (PCDDB)
http://pcddb.cryst.bbk.ac.uk

2Struc: The secondary structure server
http://2struc.cryst.bbk.ac.uk

DichroMatch: matching spectra against known reference data
http://pcddb.cryst.bbk.ac.uk/dichromatch.php

ValiDichro: CD dta validation and quality control
http://valispec.cryst.bbk.ac.uk/circularDichroism/ValiDichro/upload.html

PDBMD2CD
https://pdbmd2cd.cryst.bbk.ac.uk/

PDB2CD
https://pdb2cd.cryst.bbk.ac.uk/

Back to the top

Software Methods References:
Some of these links may have broken over the course of time, but we leave them as they are mentioned in publications.

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

Neural Network Servers

K2d web-interface
Requires a single column of cd data

K2D2 web-interface
Requires a single column of cd data from 190 or 200nm to 240nm; method updated from the original K2d.

K2D3 web-interface
An update of K2D2 with more flexible input.

Back to the top

References ...
 

  • Greenfield et al 1996 "Methods to estimate conformation of proteins and polypeptides from CD data" Analytical Biochemistry March 1st 235 (1) 1-10


    • PubMed Abstract
  • Hennesey & Johnson 1981 "Information Content in the Circular Dichroism of Proteins" Biochemistry 20 5 1085-1094


    • PubMed Abstract
  • Johnson WC 1999 "Analysing Protein Circular Dichroism Spectra for Accurate Secondary Structures" Proteins May 15 35(3) 307-312


    • PubMed Abstract
  • King S M & Johnson W C 1999 "Assigning Secondary Structure From Protein Coordinate data" Proteins: Structure, Function and Genetics 35:313-320


    • PubMed Abstract
  • Manavalan & Johnson 1987 "Variable Selection Method Improves the Prediction of Protein Secondary Structure from Circular Dichroism Spectra" Analystical Biochemistry 167 76-85


    • PubMed Abstract
  • Pancoska, Janota & Kiederling 1999 "Novel Matrix Descriptor for Secondary Structure Segments in Proteins: Demonstration of Prediction from Circular Dichroism Spectra" Analytical Biochemistry 267 72-83


    • PubMed Abstract
  • Pancoska, Sritana C, Yasui, Keiderling TA 1991 "Statistical Analysis of Vibrational  Circular Dichroism of Selected Proteins and Relationship with Secondary Structures" Biochemistry 30 5089-5103


    • PubMed Abstract
  • Perczel, Hollosi, Gabor, Tusnady, Fasman 1991 "Convex constraint analysis: a natural deconvolution of circular dichroism curves of proteins" Protein Engineering vol 4 6 669-679


    • PubMed Abstract
  • Perczel A, Park K & Fasman 1992 "Analysis of the Circular Dichroism Spectrum of Proteins Using Convex Constraint Algorithm: A Practical Guide" Analytical Biochemistry May 15 203 (1) 83-93


    • PubMed Abstract
  • Pribic R 1994 "Principle component factor analysis using Fourier Transform and or Circular Dichroism Spectra of protein secondary structure" Analytical Biochemistry Nov 15 223(1) 26-34


    • PubMed Abstract
  • Provencher & Glockner 1981 "Estimation of Globular Protein Secondary Structure from Circular Dichroism" Biochemistry 20 33-37


    • PubMed Abstract
  • Reed & Reed 1997 "A set of constructed type spectra for the practical estimation of peptide secondary structure from CD" Analytical Biochemistry Dec 1 254 (1) 36-40


    • PubMed Abstract
  • Sreerama N 1993 "A self consistent method for analysis of protein secondary structure from CD" Analytical Biochemistry Feb 15 209(1) 32-44


    • PubMed Abstract
  • Sreerama N, Venyaminov SW, Woody RW 1999 "Estimation of number of a helical and b strand segments in proteins using CD spectra" Protein Science  Feb 8 (2) 370-380


    • PubMed Abstract
  • Sreerama N & Woody RW 1994 "Protein secondary structure from Circular Dichroism Spectroscopy: Combining Variable Selection Principle and Cluster Analysis with Neural Networks, Ridge Regression and Self-consistent Methods" JMB Sep 30 242(4) 497-507


    • PubMed Abstract
  • Van Stokkum I, Spoelder, H J W, Bloemendal M, Van Grondelle, Groen F 1990 "Estimation of protein secondary structure and error analysis from CD spectra" Analytical Biochemistry Nov 15 191(1) 110-118


    • PubMed Abstract
  • Venyaminov S W, Baikalov I, Chuen-Shang C, & Yang J T, 1991 "Some problems of CD analysis of protein conformation" Analytical Biochemistry Nov 1 198(2) 250-5


    • PubMed Abstract
     
Back to the top