Protein-protein interaction modeling.
# [Prody] (http://prody.csb.pitt.edu)
sudo pip install -U ProDy
# Protein structure data
# [Zlab Benchmark] (http://zlab.umassmed.edu/benchmark/)
cd Data/
wget http://zlab.umassmed.edu/benchmark/benchmark4.tgz
tar xzf benchmark4.tgzIt may be convenient to place all version benchmark data in one place, like below:
cd benchmark4
mkdir unbound
mkdir bound
cp structures/*/*_[rl]_b.pdb bound/.
cp structures/*/*_[rl]_u.pdb unbound/.An example
bash Scripts/analyze-binders.sh Data/Docking/20140919_M2.5.3/1ACB_r_u/ Data/benchmark4/unbound/1ACB_l_u.pdb Configs/yuri.cfgYou can find your results in:
Data/Docking/20140919_M2.5.3/1ACB_r_u/classify_results.txt
ignore followings ..
python contactmap.py <docking_output_file> <partner_pdb_file>partner_pdb_file
explanation comes here..
Note A docking output file has a set of pdb files docked. You need to have these files in the correct path.