Interpretation of results

[JinyuanSun]

what does PROT_IDX_LIST indicate in the salt bridge? Also, the format is a little strange. For other records, the first 6 columns remain the same and in the salt bridge, the PROT_IDX_LIST came in.... For example:

Prediction of noncovalent interactions for PDB structure 1O41
=============================================================
Created on 2022/04/14 using PLIP v2.2.2

If you are using PLIP in your work, please cite:
Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294
Analysis was done on model 1.

300:A:300 (300) - SMALLMOLECULE
-------------------------------
Interacting chain(s): A


**Hydrophobic Interactions**
+-------+---------+----------+-----------+-------------+--------------+------+--------------+---------------+------------------------+------------------------+
| RESNR | RESTYPE | RESCHAIN | RESNR_LIG | RESTYPE_LIG | RESCHAIN_LIG | DIST | LIGCARBONIDX | PROTCARBONIDX | LIGCOO                 | PROTCOO                | 
+=======+=========+==========+===========+=============+==============+======+==============+===============+========================+========================+
| 60    | HIS     | A        | 300       | 300         | A            | 3.63 | 859          | 479           | 18.237, 26.326, 21.083 | 15.096, 24.838, 22.122 | 
+-------+---------+----------+-----------+-------------+--------------+------+--------------+---------------+------------------------+------------------------+


**Hydrogen Bonds**
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+
| RESNR | RESTYPE | RESCHAIN | RESNR_LIG | RESTYPE_LIG | RESCHAIN_LIG | SIDECHAIN | DIST_H-A | DIST_D-A | DON_ANGLE | PROTISDON | DONORIDX | DONORTYPE | ACCEPTORIDX | ACCEPTORTYPE | LIGCOO                 | PROTCOO                | 
+=======+=========+==========+===========+=============+==============+===========+==========+==========+===========+===========+==========+===========+=============+==============+========================+========================+
| 37    | GLU     | A        | 300       | 300         | A            | False     | 1.91     | 2.87     | 164.38    | True      | 304      | Nam       | 868         | O2           | 14.608, 29.056, 17.032 | 14.201, 29.694, 14.260 | 
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+


**Water Bridges**
+-------+---------+----------+-----------+-------------+--------------+----------+----------+-----------+-------------+-----------+-----------+-----------+--------------+--------------+-----------+------------------------+------------------------+------------------------+
| RESNR | RESTYPE | RESCHAIN | RESNR_LIG | RESTYPE_LIG | RESCHAIN_LIG | DIST_A-W | DIST_D-W | DON_ANGLE | WATER_ANGLE | PROTISDON | DONOR_IDX | DONORTYPE | ACCEPTOR_IDX | ACCEPTORTYPE | WATER_IDX | LIGCOO                 | PROTCOO                | WATERCOO               | 
+=======+=========+==========+===========+=============+==============+==========+==========+===========+=============+===========+===========+===========+==============+==============+===========+========================+========================+========================+
| 14    | ARG     | A        | 300       | 300         | A            | 3.97     | 3.89     | 124.85    | 93.19       | True      | 122       | Ng+       | 865          | O3           | 1009      | 17.019, 28.450, 21.059 | 16.183, 32.806, 23.298 | 16.179, 31.997, 19.494 | 
+-------+---------+----------+-----------+-------------+--------------+----------+----------+-----------+-------------+-----------+-----------+-----------+--------------+--------------+-----------+------------------------+------------------------+------------------------+
| 36    | SER     | A        | 300       | 300         | A            | 3.87     | 3.58     | 102.78    | 81.29       | True      | 303       | O3        | 870          | O3           | 1006      | 16.714, 29.756, 18.159 | 16.359, 27.696, 13.614 | 19.266, 28.707, 15.448 | 
+-------+---------+----------+-----------+-------------+--------------+----------+----------+-----------+-------------+-----------+-----------+-----------+--------------+--------------+-----------+------------------------+------------------------+------------------------+
| 37    | GLU     | A        | 300       | 300         | A            | 3.10     | 2.66     | 137.88    | 77.69       | False     | 870       | O3        | 311          | O2           | 1009      | 16.714, 29.756, 18.159 | 14.504, 33.563, 17.409 | 16.179, 31.997, 19.494 | 
+-------+---------+----------+-----------+-------------+--------------+----------+----------+-----------+-------------+-----------+-----------+-----------+--------------+--------------+-----------+------------------------+------------------------+------------------------+
| 38    | THR     | A        | 300       | 300         | A            | 3.98     | 3.83     | 108.06    | 116.81      | True      | 313       | Nam       | 869          | O3           | 1010      | 16.731, 27.749, 16.658 | 16.328, 30.876, 12.945 | 17.968, 31.516, 16.349 | 
+-------+---------+----------+-----------+-------------+--------------+----------+----------+-----------+-------------+-----------+-----------+-----------+--------------+--------------+-----------+------------------------+------------------------+------------------------+
| 38    | THR     | A        | 300       | 300         | A            | 2.82     | 3.83     | 108.06    | 85.72       | True      | 313       | Nam       | 870          | O3           | 1010      | 16.714, 29.756, 18.159 | 16.328, 30.876, 12.945 | 17.968, 31.516, 16.349 | 
+-------+---------+----------+-----------+-------------+--------------+----------+----------+-----------+-------------+-----------+-----------+-----------+--------------+--------------+-----------+------------------------+------------------------+------------------------+
| 62    | LYS     | A        | 300       | 300         | A            | 2.97     | 3.27     | 160.91    | 85.19       | True      | 505       | N3        | 869          | O3           | 1006      | 16.731, 27.749, 16.658 | 20.388, 25.699, 14.804 | 19.266, 28.707, 15.448 | 
+-------+---------+----------+-----------+-------------+--------------+----------+----------+-----------+-------------+-----------+-----------+-----------+--------------+--------------+-----------+------------------------+------------------------+------------------------+


**Salt Bridges**
+-------+---------+----------+---------------+-----------+-------------+--------------+------+-----------+-----------+-------------------------+------------------------+------------------------+
| RESNR | RESTYPE | RESCHAIN | PROT_IDX_LIST | RESNR_LIG | RESTYPE_LIG | RESCHAIN_LIG | DIST | PROTISPOS | LIG_GROUP | LIG_IDX_LIST            | LIGCOO                 | PROTCOO                | 
+=======+=========+==========+===============+===========+=============+==============+======+===========+===========+=========================+========================+========================+
| 34    | ARG     | A        | 285,287,288   | 300       | 300         | A            | 4.33 | True      | Phosphate | 867,867,864,868,869,870 | 15.906, 28.596, 17.664 | 11.817, 27.565, 18.631 | 
+-------+---------+----------+---------------+-----------+-------------+--------------+------+-----------+-----------+-------------------------+------------------------+------------------------+

Any suggestion on parsing this file?

[pslacerda]

I don't know about the salt bridges, but if you want to parse I suggest to use the -x option to output an XML file.

[juliaLopanskaia]

I wrote the code that parses xml file and gives a dataframe of interactions to easily compare several PLIP outputs. Example of output:

RESIDUE	6LSN	5XAF
hydrogen_bonds_181VAL_A	NaN	+
hydrogen_bonds_251ASP_B	+	+
hydrophobic_interactions_248LEU_B	+	+
hydrophobic_interactions_250ALA_B	+	+
hydrophobic_interactions_254LYS_B	+	+
hydrophobic_interactions_255LEU_B	+	+
hydrophobic_interactions_258ASN_B	+	+
hydrophobic_interactions_316ALA_B	NaN	+
hydrophobic_interactions_352LYS_B	+	+

There is my gist with this code at github: https://gist.github.com/juliaLopanskaia/efbe5a4935f84f72c0c160a3d6ae32ad Hope it helps someone

[JinyuanSun]

@juliaLopanskaia Wow, great job! Thanks a lot!