The deep learning method for ranking protein structural models
(1) Download DeepRank3 package (short path is recommended)
git clone https://github.com/jianlin-cheng/DeepRank3.git
(If fail, try username) git clone https://[email protected]/jianlin-cheng/DeepRank3.git
cd DeepRank3
(2) Activate your python2.7 environment, setup the tools and download the database (required)
a. edit setup_database.pl
(i) Manually create folder for database (i.e., /data/commons/DeepRank_db_tools/)
(ii) Set the path of variable '$DeepRank_db_tools_dir' for multicom databases and tools (i.e., /data/commons/DeepRank_db_tools/).
b. perl setup_database.pl
Please refer to 'cite_methods_for_publication.txt' to cite the methods that you use in DeepRank3 system for publication. The tools can be also downloaded from their official websites.
(3) Configure DeepRank3 system (required)
a. edit configure.pl
b. set the path of variable '$DeepRank_db_tools_dir' for multicom databases and tools (i.e., /data/commons/DeepRank_db_tools/).
c. save configure.pl
perl configure.pl
(4) Check whether your python environment is installed successfully (required)
source DeepRank_db_tools/tools/python_virtualenv/bin/activate
(4a) If not, use following command to manually install
sh installation/DeepRank_manually_install_files/P4_python_virtual.sh
(5) Set theano as backend for keras (required)
Change the contents in '~/.keras/keras.json'.
$ mkdir ~/.keras
$ vi ~/.keras/keras.json
{
"epsilon": 1e-07,
"floatx": "float32",
"image_data_format": "channels_last",
"backend": "theano"
}
(6) Activate your python3.6 environment and manually install deepdist tool
cd tools/deepdist
a. python setup.py
b. python configure.py
c. sh installation/set_env.sh
(7) Manually install DistRank tool
cd ../DistRank
mkdir env
python configure.py
sh installation/set_env.sh
(8) Run DeepRank3 for quality assessment
Usage:
$ sh bin/DeepRank3_Cluster.sh <target id> <file name>.fasta <model directory> <output folder>
Example:
$ sh bin/DeepRank3_Cluster.sh T0953s1 examples/T0953s1.fasta examples/T0953s1 examples/test_out
$ sh bin/DeepRank3_SingleQA.sh T0953s1 examples/T0953s1.fasta examples/T0953s1 examples/test_out
$ sh bin/DeepRank3_SingleQA_lite.sh T0953s1 examples/T0953s1.fasta examples/T0953s1 examples/test_out