I have been measuring circular dichroism spectra between 250 and 190 nm for proteins. I would like to calculate the percentage of each secondary structure element . Does anyone know any software that will do that?
Thank you so much!
Carlos.
Hi Carlos,
There appear to be quite a few tools for this kind of thing. If you can trim your data from 190-240, you could easily try K2D2 - http://cbdm-01.zdv.uni-mainz.de/~andrade/k2d2/.
There's also DiChroWeb which can be found at http://dichroweb.cryst.bbk.ac.uk/html/process.shtml. For further software check out http://dichroweb.cryst.bbk.ac.uk/html/links.shtml#soft.
There appear to be many more to choose from as well. Hope this helps!
Thank you so much for the help, Kyle.
I will try with these tools!
Carlos!
Hi Carlos,
I have got good experience with the CDPro program suite (http://sites.bmb.colostate.edu/sreeram/CDPro/), which is also on Kyle's list. It only runs on windows computers, but it has the advantage that no registration is needed.
One has to pay attention to convert the CD data to the correct units (per residue molar absorbance units (De M-1 cm-1)). Machine units in mdeg will give wrong results.
It might be worth to extend you CD measurements down to 185 or 180 nm, if possible, as this will increase the accuracy of the results significantly.
Regards, Andreas
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