PIPENN: Protein Interface Prediction with an Ensemble of Neural Nets

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

Bas Stringer*, Hans de Ferrante, Sanne Abeln, Jaap Heringa, K. Anton Feenstra and Reza Haydarlou* (2022).
Bioinformatics 38, 2111-2118. PIPENN: Protein Interface Prediction from sequence with an Ensemble of Neural Nets.

* equal contribution.

PIPENN stands for 'Protein Interface Prediction with an Ensemble of Neural Nets'. PIPENN is a set of various DL methods for predicting protein bindings of different interaction types (protein-protein, protein-small-molecule, protein-nucleotide (DNA/RNA)) at residue-level, using only information from a protein sequence.

We have created a web-server "PIPENN: Protein Interface Prediction from sequence with an Ensemble of Neural Nets" which allows you to try out your queries of interest. Typical runtimes per protein are on the order of 10 minutes.

The download link below leads to the various (large) datasets and pretrained models. The accompanying source code is available from github.com/ibivu/pipenn.

♥ Download Description MD5 PIPENN/ Download location for datasets and trained models from Stringer et al., 2021 md5 checksums README.md README file directly. LICENSE LICENSE separately. GNU General Public License v3.0 - GNU Project - Free Software Foundation (FSF).txt GNU GPL v3.0 - Free Software Foundation (FSF) 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) 2021 Bas Stringer bas.stringer.bio@gmail.com, 
                       Hans de Ferrante hansdeferrante@outlook.com, 
                       Sanne Abeln s.abeln@vu.nl, 
                       Jaap Heringa j.heringa@vu.nl, 
                       K. Anton Feenstra k.a.feenstra@vu.nl, 
                       Reza Haydarlou r.haydarlou@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/.