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Hermes Preprint: https://www.biorxiv.org/content/10.1101/640656v1

~ Due to GitHub file size limits, this repository contains a version of Hermes without the mechanism to deal with individual Protein layer server crashes. The full version is avalible as a zipped folder from Google Drive: https://drive.google.com/open?id=1qZqc_CsFrsQbkZkCWI6_fVnOpMzjaLBU

  1. Download the master branch
  2. Run the file "Houston.py"
  3. Results are given as output to the console

Dependencies

Python Version: 3.6.2

Required Python Packages

Name: Tensorflow Version: 1.5.0 URL Access: https://pypi.org/project/tensorflow/1.5.0/

Name: beautifulsoup4 Version: 4.6.0 URL Access: https://pypi.org/project/beautifulsoup4/4.6.0/

Name: requests Version: 2.17.3 URL Access: https://pypi.org/project/requests/2.17.3/

Name: imaplib2 Version: 2.45.0 URL Access: https://pypi.org/project/imaplib2/2.45.0/

Name: numpy Version: 1.13.1 URL Access: https://pypi.org/project/numpy/1.13.1/

Name: Keras Version: 2.1.3 URL Access: https://pypi.org/project/Keras/2.1.3/

Files Provided

  1. Houston.py • The laucher file

  2. Hermes_Main.py • The core pipeline, intitated by the launcher

  3. Sample_DNA_Seqs_For_Hermes.Fa • Multiple DNA sequences, given in FASTA format, to provide an initial run

  4. triplet.txt • The codon table as a text file, which is used internally

  5. 1Letter.txt • The one-letter amino acid codes as a text file, again used internally

  6. /Structure Layer Neural Network Weights - Models/Structure_Layer_BiLSTM.tfl • The Bidirectional LSTM (BiLSTM) classifier weights & biases of the Structure layer

  7. /Structure Layer Neural Network Weights - Models/Structure_Layer_CNN.tfl • The Convolutional Neural Network (CNN) classifier weights & biases of the Structure layer

  8. /Structure Layer Neural Network Weights - Models/Structure_Layer_GRU.tfl • The Gated Recurrent Unit (GRU) classifier weights & biases of the Structure layer

  9. /Structure Layer Neural Network Weights - Models/Structure_Layer_MLP.pickle • The Multilayer Perceptron (MLP) classifier weights & biases of the Structure layer

  10. /Structure Layer Neural Network Weights - Models/Structure_Layer_RNN.tfl • The Recurrent Neural Network (RNN) classifier weights & biases of the Structure layer

  11. /Structure Layer Neural Network Weights - Models/Hermes_Aggregator_Model.tfl • The final aggregator network weights & biases, a BiLSTM classifier

  12. /Hermes Results/Hermes_Result_d23481bb7250fb.txt • A text file, serving as a single example within the cashe system, that is used to save protein layer predictions

  13. /Hermes Results/Hermes_Result_facff3fc114cb2.txt • Another text file, serving as a second example within the cashe system, that is used to save protein layer predictions

  14. /Evaluation Files/JPRED Blind Test/All JPRED Blind Test Predictions w SOV Scores Redundancy Reduced.txt • A text file of all JPRED Blind test proteins, with all predictions, respective Q3's, and the experimentally determined DSSP-classified structure

  15. /Evaluation Files/JPRED Blind Test/All JPRED Blind Test NEFF & Identity Values • A text file of all NEFF & identity values for all the JPRED Blind test proteins

  16. /Evaluation Files/CASP11/All CASP11 Predictions w SOV Scores Redundancy Reduced.txt • A text file of all CASP11 proteins, with all predictions, respective Q3's, and the experimentally determined DSSP-classified structure

  17. /Evaluation Files/CASP11/All CASP11 NEFF & Identity Values • A text file of all NEFF & identity values for all the CASP11 proteins

  18. /Evaluation Files/CASP12/All CASP12 Predictions Minus SSpro w SOV Scores Redundancy Reduced.txt • A text file of all CASP12 proteins, with all predictions except for SSpro, respective Q3's, and the experimentally determined DSSP-classified structure

  19. /Evaluation Files/CASP12/All CASP12 NEFF & Identity Values • A text file of all NEFF & identity values for all the CASP12 proteins

  20. /Evaluation Files/CASP13/All CASP13 Predictions w SOV Scores Redundancy Reduced.txt • A text file of all CASP13 proteins, with all predictions, respective Q3's, and the experimentally determined DSSP-classified structure

  21. /Evaluation Files/CASP13/All CASP13 NEFF & Identity Values • A text file of all NEFF & identity values for all the CASP13 proteins

  22. /Evaluation Files/7-Fold Cross Validation/7-Fold CV Model 1.tfl-7-Fold CV Model 7.tfl • Seven files, each a set of weights & biases for the respective cross-validation model

  23. /Evaluation Files/Training/All Training Predictions w SOV Scores Redundancy Reduced.txt • A text file of all Training proteins, with all predictions, respective Q3's, and the experimentally determined DSSP-classified structure

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