I have to study the secondary structure of the protein using CD spectroscopy. However, for the analysis of data, I need CD pro software. I have found some information online regarding the software but its seems like an algorithm. So I want to know:
Is it available online (free or paid)?
How to use CD pro software?
What kind of data do I need (format)?
Thanks
Dear Sir. Concerning your issue about the CD pro software (Circular Dichroism) to determine the secondary structure of protein. CDPro software package consists of three of the popular programs (softwares) for analyzing the protein CD spectra for determining the secondary structure fractions (SELCON3, CDSSTR,and CONTIN) and a program for determining tertiary structure class (CLUSTER). These programs can now be run in a browser (Netscape Navigator or Internet Explorer) environment with ease.The program CONTIN has been modified to include the variable selection of reference proteins in the locally linearized model. The valid solutions from the variable selection are selected using the new selection rule (Helix_Rule) proposed by Johnson. This new selection rule is also incorporated in SELCON3.
One of the major problems in using different programs for CD analysis has been the use of different reference proteins and different assignments of secondary structures in different softwares. The programs provided here have been modified to accept any given set of reference proteins (CD spectra and secondary structure fractions), and seven such reference sets (constructed from the reference sets generally used in CD analysis) are provided. An eighth set can be constructed based upon the tertiary structure class. Moreover, input data files for these three programs are identical, requiring the creation of a single input file (INPUT).
Estimates of alpha-helix, bete-sheet, turns and poly(Pro)II secondary structures can be obtained from CD analysis. Number of alpha-helical and beta-strand segments can aso be estimated. Calculated CD spectral data (along with RMSD and NRMSDwith experimental data) from the three programs are output for easy incorporation into a graphics software. RMSD and NRMSD from the three programs decrease in the order:
SELCON3 > CDSSTR > CONTINLL. (Use caution in interpreting RMSDandNRMSD!)
Two new reference sets, constructed by including membrane proteins, are also provided. I think the following below links may help you in your analysis:
http://dichroweb.cryst.bbk.ac.uk/html/links.shtml
http://sites.bmb.colostate.edu/sreeram/CDPro/
http://sites.bmb.colostate.edu/sreeram/CDPro/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728378/
Thanks
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