PLIP

[root@rockylinux ~]# dnf install apptainer apptainer-suid
 
[root@rockylinux ~]# mkdir /apps/PLIP
 
[root@rockylinux ~]# cd /apps/PLIP
 
[root@rockylinux PLIP]#
[root@rockylinux PLIP]# wget https://github.com/pharmai/plip/releases/download/v2.2.2/plip_v2.2.2.simg
 
[root@rockylinux PLIP]# chmod +x plip_v2.2.2.simg

[saber@rockylinux ~]$ mkdir PLIP
[saber@rockylinux ~]$ cd PLIP
 
[saber@rockylinux PLIP]$ 
[saber@rockylinux PLIP]$ /apps/PLIP/plip_v2.2.2.simg
usage: PLIP [-h] (-f INPUT [INPUT ...] | -i PDBID [PDBID ...])
            [-o OUTPATH | -O] [--rawstring] [-v] [-q] [-s] [-p] [-x] [-t] [-y]
            [--maxthreads MAXTHREADS] [--breakcomposite] [--altlocation]
            [--nofix] [--nofixfile] [--nopdbcanmap] [--dnareceptor]
            [--name OUTPUTFILENAME] [--peptides PEPTIDES [PEPTIDES ...] |
            --intra INTRA] [--keepmod] [--nohydro] [--model MODEL]
PLIP: error: one of the arguments -f/--file -i/--input is required
 
[saber@rockylinux PLIP]$

[saber@rockylinux PLIP]$ /apps/PLIP/plip_v2.2.2.simg -i 1vsn -yv
2023-05-14 00:16:23,460 [INFO] [plipcmd.py:124] plip: Protein-Ligand Interaction Profiler (PLIP) 2.2.2
2023-05-14 00:16:23,460 [INFO] [plipcmd.py:125] plip: brought to you by: PharmAI GmbH (2020-2021) - www.pharm.ai - hello@pharm.ai
2023-05-14 00:16:23,460 [INFO] [plipcmd.py:126] plip: 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
2023-05-14 00:16:23,461 [INFO] [webservices.py:41] plip.exchange.webservices: downloading file from PDB
2023-05-14 00:16:24,300 [INFO] [plipcmd.py:99] plip: file downloaded as ./1vsn.pdb
2023-05-14 00:16:24,300 [INFO] [plipcmd.py:49] plip: starting analysis of 1vsn.pdb
2023-05-14 00:16:24,309 [DEBUG] [supplemental.py:397] plip.basic.supplemental: detected pdb as format, trying to read file with OpenBabel
2023-05-14 00:16:24,449 [DEBUG] [supplemental.py:414] plip.basic.supplemental: molecule successfully read
2023-05-14 00:16:24,451 [INFO] [preparation.py:1372] plip.structure.preparation: PDB structure successfully read
2023-05-14 00:16:24,451 [DEBUG] [preparation.py:1383] plip.structure.preparation: PyMOL name set as: 1vsn
2023-05-14 00:16:24,454 [DEBUG] [preparation.py:410] plip.structure.preparation: 1 ligand(s) after first filtering step
2023-05-14 00:16:24,454 [DEBUG] [preparation.py:271] plip.structure.preparation: 1 ligand kmer(s) detected for closer inspection
2023-05-14 00:16:24,455 [DEBUG] [preparation.py:298] plip.structure.preparation: finalizing extraction for ligand NFT:A:283 with 1 elements
2023-05-14 00:16:24,455 [DEBUG] [preparation.py:309] plip.structure.preparation: ligand classified as SMALLMOLECULE
2023-05-14 00:16:24,455 [DEBUG] [preparation.py:322] plip.structure.preparation: hetero atoms determined (n=33)
2023-05-14 00:16:24,455 [DEBUG] [preparation.py:333] plip.structure.preparation: atom neighbours mapped
2023-05-14 00:16:24,455 [DEBUG] [preparation.py:358] plip.structure.preparation: renumerated molecule generated
2023-05-14 00:16:24,457 [DEBUG] [supplemental.py:317] plip.basic.supplemental: number of isomorphisms: 96
2023-05-14 00:16:24,465 [INFO] [preparation.py:1399] plip.structure.preparation: protonated structure written to ./1vsn_protonated.pdb
2023-05-14 00:16:24,468 [INFO] [preparation.py:1420] plip.structure.preparation: analyzing one ligand
2023-05-14 00:16:24,468 [INFO] [preparation.py:1442] plip.structure.preparation: processing ligand NFT [SMALLMOLECULE] -- NFT:A:283
2023-05-14 00:16:24,475 [DEBUG] [preparation.py:549] plip.structure.preparation: number of aromatic ring candidates: 2
2023-05-14 00:16:24,476 [INFO] [preparation.py:1034] plip.structure.preparation: contains 2 aromatic ring(s)
2023-05-14 00:16:24,485 [INFO] [preparation.py:1148] plip.structure.preparation: ligand contains 3 halogen atom(s)
2023-05-14 00:16:24,525 [INFO] [preparation.py:1481] plip.structure.preparation: binding site atoms in vicinity (7.5 A max. dist: 171)
2023-05-14 00:16:24,527 [DEBUG] [preparation.py:549] plip.structure.preparation: number of aromatic ring candidates: 41
2023-05-14 00:16:24,549 [INFO] [preparation.py:789] plip.structure.preparation: reduced number of hydrophobic contacts from 9 to 4
2023-05-14 00:16:24,590 [INFO] [preparation.py:672] plip.structure.preparation: ligand interacts with 9 binding site residue(s) in chain(s) ['A']
2023-05-14 00:16:24,590 [INFO] [preparation.py:693] plip.structure.preparation: complex uses ['7 hydrogen bond(s)', '2 halogen bond(s)', '2 water bridge(s)']
2023-05-14 00:16:24,758 [DEBUG] [visualize.py:44] plip.visualization.visualize: setting current_name to 1vsn and PDB-ID to 1vsn
2023-05-14 00:16:24,758 [DEBUG] [visualize.py:51] plip.visualization.visualize: selecting ligand for PDBID 1vsn and ligand name Ligand_NFT
2023-05-14 00:16:24,758 [DEBUG] [visualize.py:52] plip.visualization.visualize: resn NFT and chain A and resi 283
 Executive: object "1vsnCartoon" created.
 Executive: object 1vsnCartoon created.
2023-05-14 00:16:24,785 [INFO] [plipcmd.py:163] plip: finished analysis, find the result files in the working directory
 
[saber@rockylinux PLIP]$
[saber@rockylinux PLIP]$ ls -l
total 1844
-rw-rw-r--. 1 saber saber 1229564 May 14 00:16 1VSN_NFT_A_283.pse
-rw-rw-r--. 1 saber saber  188649 May 14 00:16 1vsn.pdb
-rw-rw-r--. 1 saber saber  459879 May 14 00:16 1vsn_protonated.pdb
 
[saber@rockylinux PLIP]$

[saber@rockylinux PLIP]$ pymol 1VSN_NFT_A_283.pse