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SOMCD: Method for evaluating protein secondary structure from UV circular dichroism spectra

✍ Scribed by Per Unneberg; Juan J. Merelo; Pablo Chacón; Federico Morán

Publisher
John Wiley and Sons
Year
2001
Tongue
English
Weight
297 KB
Volume
42
Category
Article
ISSN
0887-3585

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✦ Synopsis

This article presents SOMCD, an improved method for the evaluation of protein secondary structure from circular dichroism spectra, based on Kohonen's self-organizing maps (SOM). Protein circular dichroism (CD) spectra are used to train a SOM, which arranges the spectra on a two-dimensional map. Location in the map reflects the secondary structure composition of a protein. With SOMCD, the prediction of beta-turn has been included. The number of spectra in the training set has been increased, and it now includes 39 protein spectra and 6 reference spectra. Finally, SOM parameters have been chosen to minimize distortion and make the network produce clusters with known properties. Estimation results show improvements compared with the previous version, K2D, which, in addition, estimated only three secondary structure components; the accuracy of the method is more uniform over the different secondary structures.

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