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Protein Contact Prediction using Dilated Convolutional Neural Networks with Dropout

Project description

DEEPCON: Protein Contact Prediction using Dilated Convolutional Neural Networks with Dropout

Contact:

Email: adhikarib@umsl.edu
Homepage: https://badriadhikari.github.io/
Paper: https://www.biorxiv.org/content/10.1101/590455v1

DEEPCON using Covariance features as input

Trained and validated using the 3456 proteins in the DeepCov dataset with the covariance features (441 channels) as input.

Installation Instructions:

You need a deep learing backend that is Keras compatible:

pip3 install -U tensorflow
pip3 install pyyaml

Install DEEPCON-Covariance package

pip3 install deepcon

Intstructions for User:

Inside Python:

import deepcon

Predict

python ../deepcon-covariance.py --aln ./16pkA0.aln --rr ./16pkA0.rr

Evaluate

./coneva-lite.pl -pdb ./16pkA.pdb -rr ./16pkA0.rr

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