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

Bioinformatics. 2007 Feb 1;23(3):385-6. doi: 10.1093/bioinformatics/btl610. Epub 2006 Nov 30.


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).

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

Supplementary information: http://gpcr.biocomp.unibo.it/~emidio/K-Fold/K-Fold_help.html.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Computer Graphics
  • Computer Simulation
  • Kinetics
  • Models, Chemical*
  • Models, Molecular*
  • Protein Conformation
  • Protein Folding
  • Proteins / chemistry*
  • Proteins / ultrastructure*
  • Software*
  • User-Computer Interface*


  • Proteins