From Rost Lab Open
Revision as of 15:54, 19 October 2014 by Hampt (talk | contribs)


Profppikernel uses an accelerated version of the original profile kernel [1] to automatically train SVM based protein-protein interaction (PPI) prediction models.

The main executable is profppikernel.

It uses profkernel-core ([accelarated profile kernel fastprofkernel]) and trains or applies a SVM based PPI prediction model model. It provides two modes of operation. In the first mode, 'training', the user provides evolutionary protein profiles and PPIs between them (labels) as input and profppikernel outputs a folder with all model files required for predictions. In the second mode, 'prediction', the user provides the path to such a model folder and to the query profiles and PPIs. profppikernel then predicts their probability to interact.


We have included both executables in a Debian package, together with man pages and a sample classification problem. There are two common ways to install it.

  • Via our Debian repository (package "fastprofkernel").
  • By manual download and installation of the binary .deb package (please see the manual of your distribution for how to install .deb packages).

For installation on non-Debian based systems, you can download the .tar.gz source package and compile and install it with the included make based installation (see the README file).

Bugs and Other Issues

Please report bugs and other issues via Bugzilla.


T. Hamp, T. Goldberg and Rost, B. (2013): Accelerating the Original Profile Kernel. PLoS One, 8(4), e68459


For questions, please contact