Interaction Filtering

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This is the 1st version (20200210) of Interaction Filtering. Please copy the code to your current directory.

$ cp -r /mnt/nfs/home/sgu/code/interfilter .

To run the code, you need OpenEye (version 2019.Oct.2). You can follow the instruction to install:

On our cluster, you may source my environment.

$ source /nfs/home/sgu/anaconda3/etc/profile.d/conda.csh
$ conda activate oepython
$ setenv OE_LICENSE /nfs/soft/openeye/oe_license.txt

If you find any version conflicts between python 3.7 and 2.7. You may comment in the ~/.cshrc: # source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh

Running the code:

$ python -protein rec.crg.pdb -ligand poses.mol2

If you want to know the interaction for a specific residue (e.g. ASP115A, A means chain A):

$ python -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A

If you want to plot the paired/unpaired interaction (figure generation can be slow, but several thousand should be fine):

$ python -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A -plot

thumb|center|500px|An example of paired interaction plot thumb|center|500px|An example of unpaired interaction plot

The output is a txt file, containing 15 columns: 1ligand 2clash 3hbond_clash+sbridge_clash 4unpairedl_donor+unpairedl_sbridge 5unpairedl_acceptor 6unpairedp_donor+unpairedp_acceptor 7unpairedp_sbridge 8contact 9hbond+hbond_nonideal 10hbond_ligand 11sbridge 12stacking 13cationpi 14halogen 15residue

To filter out compounds, you may be interested in:

Column3: # of hydrogen bond clash + # of salt bridge clash

Column4: # of unpaired ligand donor + # of unpaired ligand salt bridge

Column9: # of hydrogen bond + non-ideal hydrogen bond

Column11: # of salt bridge

Column15: interaction for you specified residue (0 means no, 1 means yes)