Q:
What is CDPro?
A: CDPro is a suite of programs for protein CD
analysis. It contains three popular CD analysis programs [CONTIN, CDSSTR,
and SELCON3], a program to generate INPUT file that is used
by all three programs, and a program [CLUSTER] for determining the
tertiary structure class from CD spectrum. The CD analysis programs use
multiple sets of reference proteins [CD and secondary structure data] and
these are also provided in this site. Download the CDPro.zip file and
unzip it from your C: drive. CDPro directory will be created with all
necessary files. Open the RunCDPro.html
file from a internet browser.
Q: How do I use CDPro?
A: CDPro can be used either in a PC or on any computer.
The executables and the browser-based linker for analysis are provided
at this site; download CDPro.zip. The programs need to be compiled
for any other computer. The INPUT file need to be generated before executing
the CDPro programs.
Q: What spectral range should
be used for a good analysis?
A: Normally, one should use CD spectra at least in
the range 190-240 nm. But sometimes experimental conditions limit the
range to 200 nm or so, and the flexibility of the refernce sets in the
more recent programs allows the use of 200-240 nm in CD analyses. The reliability,
however, is slightly reduced as one reduces the wavelength range. Comparison
of performances of the two spectral ranges are available in Sreerama et
al. Anal. Biochem. (2000)
Q: What are units of CD data
used in the analysis?
A: The CD spectra should be in per
residue molar absorbance units (De M-1
cm-1). Most CD instruments have the software to convert
raw CD data to either molar ellipticity or molar absorbance units. Be sure
to divide the CD data by the number of residues in the protein. The CD
data in either molar ellipticity or molar absorbance units can be
used in the CRDATA program to generate
the INPUT file.
Q: How do I generate the Input
file?
A: The analysis programs are written is FORTRAN and they
require CD data in a certain format. The file "INPUT" need to be
created containing the CD data, wavelength range, etc. It can be done using
a program called "CRDATA" which converts CD data from any CD instrument
in a text file to the required format. You will have to refer to the manual
or check the software that came with your CD instrument. The text file
should contain only wavelength and CD value in each line. Check the examples
provided.
Q: How do I choose a reference
set?
A: The reference set with the largest number of proteins
should be chosen. This often depends on your CD data. If your CD data
is only down to 190 nm or so (say, 190-250 nm) then you can select the
reference set with 43 proteins (Basis_1 = 4). But if you have CD
data down to 180 nm (180-250 nm) then it would be wise to use the reference
set with 29 proteins, which has CD data in the range 178-260 nm. Our studies
have suggested that the limitaions introduced in the analysis by the lack
of short-wavelength data (180 to 190 nm) is partially overcome by the use
of a larger reference set.
Q: Which values can I change,
and How do I change them, in the INPUT file?
A: The only values that may be changed in a properly
generated INPUT file are IPRINT (from 0 to 1)
and Basis_1 (any value between 1-8). Changing
IPRINT to 1 would generate the output for every iteration and this should
be done if a problem is suspected in the analysis; otherwise the standard
output is sufficient to examine the results. Basis_1 value determines
the reference set to be used in the analysis. Normally, the largest
reference set available for the wavelength range should be used. Value
of 8 selects a reference set based on the tertiary class determined by
the CLUSTER program which should be run prior
to its selection. Values 6 and 7 select reference sets with denatured
CD spectra, and should be used for studying CD spectra under denaturing
conditions. Consult the Readme and other help files provided. The changes
in the INPUT file can be made using a text editor; Edit_Input button
at the top of the screen can be used to open the DOS editor on your PC.
Q: How do I read the results?
A: Each program (CDSSTR, CONTINLL, and SELCON3) has a
separate output (program_name.OUT) which contains results at various stages.
Summary of the run (title, reference set, program and secondary structure)
is added to ProtSS.OUT (execution of each of these programs write to this
file). The calculated CD spectrum (corresponding to the result) is also
output -- see next Q.
Q: Can I compare the Calculated
CD spectra with Experiment?
A: Yes. The calculated CD spectrum (from each
program) is compared with the experimental spectrum in files: CalcCD.OUT,
reconCD.OUT and CONTIN.CD. They can be imported into a plotting software,
such as Axum or SigmaPlot . The programs also calculate the RMSD between
the two and print the result in program_name.out and ProtSS.out files. |