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Protein-Protein Interaction prediction using a deep RNN-based neural network architecture.

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deepsequenceppi's Introduction

DeepSequencePPI

Protein-Protein Interaction prediction using a deep RNN-based neural network architecture.

You can access our code as a Jupyter Notebook in this repository.

The AA sequence data used was obtained from Uniprot (the full reviewed database, or only the ones in the interaction datasets, you decide!).

All the interaction datasets were obtained from https://www.ncbi.nlm.nih.gov/pubmed/28514151 . In their abstract there is a link to the data we used, as well as their own code (used to replicate their experiments and compare our methods).

Feel free to ask any questions! (I will include the conference paper as well in the repository).

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deepsequenceppi's Issues

Could you share the original code and datasets ?

Thanks for your work!
I am interested in prediction of PPI, your work achieves a good effect.
The paper you mentioned 'DeepPPI: Boosting Prediction of Protein−Protein Interactions with
Deep Neural Networks' , is a great work. But unfortunately, the link they provided is invalid now, I can not obtain their code and data. Could you share the original code and datasets if possible?
My email is [email protected].

Thanks very much.

FGonzalezLopez / DeepSequencePPI

Please provide the dataset folder also if u can. I'm new to python and bioinformatic so can't find it.
And could u plz explain some steps of code in 2-3 line about what u did in particular section

trained model

Hi,
It is possible for you to upload the trained model, for testing of my given input, which you have built for your paper (http://www.ugr.es/~jamc/Files/Lopez18_PPIEmbedding.pdf).

Thanks

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