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SOMCD: Method for evaluating protein secondary structure from UV circular dichroism spectra
Author(s) -
Unneberg Per,
Merelo Juan J.,
Chacón Pablo,
Morán Federico
Publication year - 2001
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/1097-0134(20010301)42:4<460::aid-prot50>3.0.co;2-u
Subject(s) - protein secondary structure , circular dichroism , spectral line , chemistry , distortion (music) , vibrational circular dichroism , biological system , set (abstract data type) , protein structure , crystallography , pattern recognition (psychology) , artificial intelligence , computer science , physics , biology , biochemistry , amplifier , bandwidth (computing) , astronomy , programming language , computer network
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 β‐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. Proteins 2001;42:460–470. © 2001 Wiley‐Liss, Inc.