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Bioinformatics. 2007 Feb 1;23(3):385-6. Epub 2006 Nov 30.

K-Fold: a tool for the prediction of the protein folding kinetic order and rate.

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Biocomputing Group, CIRB/Department of Biology, University of Bologna, via Irnerio 42, 40126 Bologna, Italy.


K-Fold is a tool for the automatic prediction of the protein folding kinetic order and rate. The tool is based on a support vector machine (SVM) that was trained on a data set of 63 proteins, whose 3D structure and folding mechanism are known from experiments already described in the literature. The method predicts whether a protein of known atomic structure folds according to a two-state or a multi-state kinetics and correctly classifies 81% of the folding mechanisms when tested over the training set of the 63 proteins. It also predicts as a further option the logarithm of the folding rate. To the best of our knowledge, the tool discriminates for the first time whether a protein is characterized by a two state or a multiple state kinetics, during the folding process, and concomitantly estimates also the value of the constant rate of the process. When used to predict the logarithm of the folding rate, K-Fold scores with a correlation value to the experimental data of 0.74 (with a SE of 1.2).



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