This repo is for Functional PTM Predictions(cDL-FuncPhos) and Phosphorylation/Acetylation/Ubiquitination(cDL-PAU) Predictions

• 1. Purpose

  To predict Functional-PTM site(cDL-FuncPhos) or Phosphorylation/Acetylation/Ubiquitination PTM site(cDL-PAU) using deep learning method.

  2.Repo Contents

  • Datasets: All datasets.
  • Evaluation_Indicators: evaluation index functions.
  • fig: plotting ROC curves.
  • src: genarating data, traing or predicting model codes.

  3. System requirements

  Installation and running has been tested in Ubuntu 18.04.4 LST with python 3.7.7.

  Package version

  • python = 3.7.7
  • numpy = 1.18.5
  • Keras = 2.4.3
  • Tensorflow = 2.2.0

  You can install the dependent packages by the following commands:

  • pip install python==3.7.7
  • pip install numpy==1.18.5
  • pip install keras==2.4.3
  • pip install tensorflow==2.2.0

  4. Predicting

  • To predict Functional PTM site using all(seq+str+dyn) features, run the following command:

    python ./src/cDL_FuncPhos_model.py

  • To predict Phosphorylation/Acetylation/Ubiquitination PTM site using all(seq+str+dyn) features, run the following command:

    python ./src/cDL_PAU_model.py

  Training and testing data are provided in the folder of ./Datasets.

This project is licensed under the terms of the GNU General Public License v3.0 license.