EDLMPPI: Learning the Protein Language of Proteome-wide Protein-protein Binding Sites via Ensemble Deep Learning in an Interpretation Manner
conda install python==3.8.12
pip install tensorflow==2.4.1
pip install keras==2.4.3
pip install numpy==1.19.5
- Install dependencies
create a program directory
mkdir -p ../programs && cd ../program
- Install SPRINT
git clone https://github.com/lucian-ilie/SPRINT.git
git checkout DELPHI_Server
make compute_HSPs_parallel
- Install psiblast: 2.6.0+ and download the corresponding nr database. (The database used in EDLMPPI is Uniref90)
For Ubuntu:
sudo apt-get install ncbi-blast+
-
Intall hh-suite. The database used in DELPHI is uniprot20_2015_06.
-
Install GENN+ASAquick
-
Install ANCHOR
-
Run the following code to extract MBF
bash feature_computation/compute_features.sh $INPUT_FN
-
Install virtual environment
conda create -n ProtT5 pyhton=3.7 conda activate ProtT5
-
Following the steps showing in the ProtT5-XL-UniRef50.ipynb
-
Notes:
The result will be saved as .npy
-
Install virtual environment
conda create -n PPI conda activate PPI conda install python==3.8.12 pip install tensorflow==2.4.1 pip install keras==2.4.3 pip install numpy==1.19.5
-
Download the Train Data at http://www.edlmppi.top:5002/download_train
-
Following the steps showing in the /train/run.ipynb
-
Install virtual environment
conda create -n PPI conda activate PPI conda install python==3.8.12 pip install tensorflow==2.4.1 pip install keras==2.4.3 pip install numpy==1.19.5
-
The Predict Example can be download in current repository
python ./predict/pred.py
- If you want to get predicted result faster, you can go to http://www.edlmppi.top:5002/ using our online predicted tool.
- If you have any question, you can contact [email protected]
链接: https://pan.baidu.com/s/1UdpI5yENzCxgdd3ZSq66Ng?pwd=52jt 提取码: 52jt 复制这段内容后打开百度网盘手机App,操作更方便哦