Another (Not So) Wasted Effort

This is the Dicroweb, which a facility of the BBSRC Centre for Protein and Membrane Strucutre Dynamics, based in the UK. This site provides on-line Circular Dichroism (CD) analysis. I personally found it to be a great tool for CD analysis. Easy to up-load your raw data, with the web-site performing all the calculations for you (inputing mdeg and getting ellipticity measurements back (rme or other)). You do need to read a little about the types of analysis that this site offers as there are several different models to use, (CONTINLL, SELCON3, CDSSTR, VARSLC, and K2D) as well as different reference sets. But if you are doing Circular Dichroism, then you really should learn what these are (limitations etc). You will need an account, which in my case was granted in about a week or so (maybe less, it was pretty quick though).

My only problem with it was that I was analysing a 9 amino acid peptide and this site has a maximum time-limit for its analysis as they don't want to bog the server down too much. For normal proteins etc this is an excellent program and I give it my full support. For peptides though, you are trying your luck. Give it a go though, you may get lucky.

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CDPro is kind of a gold standard in CD analysis from Colorado State University. It is stand-alone, so you can download it and run it on your own computer (don't know if it runs on Macs not running Boot-camp though). It runs in your internet browser (Netscape or Internet Explorer) and uses the CONTINLL, SELCON3, and CDSSTR programs for analysis. It's use is free for not-for-profit organizations. I would try this as well, there is a new "membrane proteins" reference set included now which may be of use.
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PEPFIT. This program's development is detailed in:

Reed, J. & Reed, T.A. (1997) A set of constructed type spectra for the practical estimation of peptide secondary structure from circular dichroism. Anal. Biochem. 254, 36±40.

and it is my favorite. There is no link here because you need to get in contact with the authors of this program yourself and they will send it to you. It is an MS DOS based program designed by the authors to help in their own research, and was designed based on CD specs from peptides (as opposed to the large globular proteins used in other CD analysis programs). It allows you to guess what percentage of several types of conformations your spectra may have, and then the program overlays your guess with your actual result and gives you an error calculation.

While it's a great program, I didn't like the heavy requirement of user input, and it may take you a while to get a good fit if your peptide is a mixture of several types of beta turns.
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PEPFIT Analysis. This is a program written by myself and is entirely based on the PEPFIT program described above. This program is also stand alone, but has the advantage of running in MS Office (Excel). I have tested it in all versions of Office since 2000, and it works in all including Office 2007. You must allow macros to be run. It was written in Excel 2000, and runs best there though.

The advantages of the PEPFIT Analysis program over the original PEPFIT program is that it runs in Excel, and it is a point and click operation with minimal user intervention. I have kept the original idea of PEPFIT and allowed the user to guess the percent conformation, but I have also made the program do the guess-work for you. You simply paste the spectra values in, click the PEPFIT Analysis icon, select a few criteria (described in the accompanying documents), and away you go. You can analyze your circular dichroism data agianst all 9 reference curves, or select a few, but again, these details are described in the instruction supplied.

Your CD results are compared with combinations of the reference curves you select, and the final top 10 best fit results are presented using an R squared error calculation as the best fit criteria.

The first (well second if you include my thesis) is now in peer reviewed publication (Amon, M. A., Ali, M., Bender, V., Hall, K., Aguilar, M.-I., Aldrich-Wright, J., and Manolios, N. (2008) Kinetic and conformational properties of a novel T-cell antigen receptor transmembrane peptide in model membranes. Journal of Peptide Science).

Following suggestions from one user in particular, I am currently upgrading the program a bit by making it run a bit faster and simpler, and also, at the suggestion of one user, I am trying to add a reference curve fora polyproline helix, but this may take me a while as it's now something I do in my "spare" time while post-docking.

If you are interested in this software, you need only ask for a copy (post a comment or e-mail michael_amon@hotmail.com and use "PEPFIT Analysis" as your subject heading.
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