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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