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Seeing the Trees through the Forest:
Sequence-based Homo- and Heteromeric
Protein-protein Interaction sites prediction
using Random Forest

This is the download page for our work described in the following paper. Please read it before using our tool, and please cite it afterwards :-)

Qingzhen Hou, Paul De Geest, Wim F. Vranken1, Jaap Heringa and K. Anton Feenstra (2017). Seeing the Trees through the Forest: Sequence-based Homo- and Heteromeric Protein-protein Interaction sites prediction using Random Forest. Bioinformatics, doi: 10.1093/bioinformatics/btx005, 2017
1Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB & Structural Biology Brussels, VUB & Structural Biology Research Centre, VIB; Brussels 1050, Belgium.

We have created a web-server "SeRenDIP — SEquence-based Random forest predictor with lENgth and Dynamics for Interacting Proteins" which allows you to try out your queries of interest. However, due to the two-tiered blast searches (we need profiles for each hit in the first blast search), runtimes can be quite substantial on our server. If you need more performance, you may instead rather want to use the stand alone version supplied in the download link below.

Downloads
Hou_etal_RF-PPI_predictors_datasets.tar.gz Archive containing README, test R script, predictors and test datasets. (836MB)
README.md README file separately.

    These scripts and datafiles are provided as-is, and come without 
    any warranty whatsoever. If it works for you, great, let me know!
    If it doesn't work for you, we'd be happy to try and help you fix it. 
    If it destroys your universe, too bad (you may still file a bug report).
 
    Copyright (c) 2016 Q. Hou q.hou@vu.nl, 
                       P. De Geest pauldegeest1@gmail.com, 
                       W.F. Vranken wvranken@vub.ac.be, 
                       J. Heringa j.heringa@vu.nl, 
                       K. Anton Feenstra k.a.feenstra@vu.nl.

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see www.gnu.org/licenses/.

(c) IBIVU 2017. If you are experiencing problems with the site, please contact the webmaster.