CD tutorials

Software downloads

Other sites for online deconvolution
 

References
 

      CD Tutorials ...
 

• CD and SRCD Tutorial from the British Biophysical Society's "what is biophysics" pages.
  http://www.cryst.bbk.ac.uk/BBS/whatis/cd_website.html
   
   

• Lawrence Livermore tutorial
  http://www-structure.llnl.gov/cd/cdtutorial.htm
   
   

• Protein structure course PPS96
  http://broccoli.mfn.ki.se/pps_course_96/ss_960723_21.html
   
   

• CD Facility at University of Buffalo
  http://www.pharmacy.buffalo.edu/phc/facilities/cd
   
   

• Astbury Centre for Structural Biology at Leeds
  http://www.astbury.leeds.ac.uk/
   
   

• UNC MacInFac facility
  http://macinfac.bio.unc.edu/
   
   

• Daresbury CLRC
  http://www.srs.dl.ac.uk/VUV/CD/links.html
   
   

• Alliance Protein Laboratories
  http://www.ap-lab.com/circular_dichroism.htm
   
   

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         Software Downloads ...

  • CCA
    Convex constraint algorithm (Perczel et al)
    Available for windows platform only

  • CONTIN
    Implementation of ridge regression algorithm. Several versions available... the latest contin/ll incorporates the locally linearised model of van Stokkum et al.
    Source code available

  • CDFIT
    Linear least squares fit method configured for JASCO formatted files.
    Source code available

  • CDPRO
    Suite of programmes including the latest versions of CONTIN SELCON and CDSSTR.
    Source codes for all three are available

  • CDSSTR
    Modified version of the variable selection programme by Johnson et al (Varslc)  to utilise a number of different reference datasets.
    Source code available

  • DichroProt/Antheprot
    Suite of programmes for protein structure analysis designed for windows but with source codes available for Varslc.
    windows only

  • K2D
    Neural network approach from Andrade et al
    Source code available

  • LINCOMB
    Linear combination least squares method available with CCA
    windows only

  • SELCON
    The self-consistent method (Sreerama & Woody). Several verions available.
    Source code available

  • VARSLC
    The original version of the variable selection method by Johnson et al.
    Source code available (ftp link)

  • XTLSSTR
    A programme from Johnson  to obtain structure fractions from PDB files by analysing hydrogen bonds.
    Source code available

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         Online Deconvolution servers ...

  • K2d web-interface
    Easy to use web form, requiring a single column of cd data

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         References ...
   

  • Bohm et al 1992 "Quantitative analysis of protein far UV circular dichroism spectra by neural networks" Protein Engineering vol 5 3 191-195
  
  PubMed Abstract
  • 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
  
  
  • 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
  
  
  • 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, Venyaminoy 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 Circlar 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
   

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