RAPPPID

Regularised Automative Prediction of Protein-Protein Interactions using Deep Learning

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RAPPPID is a deep learning model for predicting protein interactions. You can read more about it in the OUP Bionformatics paper.

How to Use RAPPPID

Training New Models

It's possible to train a RAPPPID model using the train.py utility. For precise instructions, see docs/train.md.

Data

See docs/data.md for information about downloading data from the manuscript, pre-trained weights, or preparing your own datasets.

Infering

See docs/infer.md for advice on how to use RAPPPID for infering protein interaction probabilities.

Environment/Requirments

The conda environment file (environment.yml) is available in the root of this repository. This lists all the python libraries and the versions used for running RAPPPID.

Alternatively, there's a requirements.txt file if you prefer to use PIP.

You'll need an NVIDIA GPU which is CUDA compatible. RAPPPID was tested on RTX 2080, V100, and A100 GPUs.

License

RAPPPID

Regularised Automative Prediction of Protein-Protein Interactions using Deep Learning

Copyright (C) 2021 Joseph Szymborski

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero 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 Affero General Public License for more details.

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