CDNN Secondary Structure Analysis

Guidance on using CDNN CD spectra deconvolution software

CDNN is a program which can be used to analyze circular dichroism (CD) spectra. It was written by Dr. Gerald Böhm, Institut für Biotechnologie, Martin-Luther Universität Halle-Wittenberg, who has kindly agreed to let Applied Photophysics distribute the software. Please note that any publication of results calculated using CDNN should refer to the author (see CDNN manual on disk for details).


CDNN is just one of a large number of circular dichroism analysis tools which are available. A list of some alternative CD secondary structure analysis programs is provided at the end of this document. Other tools can be found by searching through Google. CDNN  can be found on the CD-ROM which was provided with your Chirascan circular dichroism spectrometer. If you do not have access to the disc, you can contact our Technical Support team at tech.support@photophysics.com to request a copy of the software.

 

Installation

Installation of the CDNN software is straightforward. Run the SETUP.EXE program and follow the instructions. Please read the Software Licence Agreement. Remember, although the software is provided by Applied Photophysics it is Copyright © Dr. Gerald Böhm.

 

Getting Started

Start the CDNN software from the shortcut on the Start Menu. You will be presented with a dialogue (see figure 1).

 

[Figure 1. CDNN CD Spectra Deconvolution Software]

Figure 1. CDNN CD Spectra Deconvolution Software

 

Click on File>Open... On first use, the program will open at the Sample Files folder (C:\Program Files\CD deconvolution\Sample files\). Select one of the sample files and click on Open. In this example the Lysozyme file lysozym.txt has been used. CDNN will present the user with a dialogue asking the user to select the CD signal type (see figure 2).

 

Figure 2. CD Signal Type dialogue

Figure 2. CD Signal Type dialogue


All the examples in the Sample Files folder are converted to Delta Epsilon, the differential extinction coefficient (in this case further normalised for the number of amino acid residues, of which more later). Click on OK. The panel will disappear and you will be left with the start-up panel. Click on Deconvolute to calculate the contributions of the various components to the protein secondary structure.

 

 Figure 3. CDNN CD Spectra Deconvolution Software

Figure 3. CDNN CD Spectra Deconvolution Software

 

The units, delta epsilon, are per amino acid residue. Once you are familiar with the use of the program and what the results mean, move on to your own samples. Note: it is highly recommended that you read the notes that come with the program itself!

The British Assessment Bureau