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


BACKGROUND
http://gpcr.biocomp.unibo.it/cgi/predictors/K-Fold/K-Fold.cgi.


BACKGROUND
http://gpcr.biocomp.unibo.it/~emidio/K-Fold/K-Fold_help.html.
Capriotti
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Biocomputing Group, CIRB/Department of Biology, University of Bologna, via Irnerio 42, 40126 Bologna, Italy. emidio@biocomp.unibo.it
Casadio
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D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D012984:Software; D014584:User-Computer Interface
D011506:Proteins