Protein Ligand Interaction Profiler
This repository contains test content and script.
JeongSoo Na. Syntekabio
원활한 PLIP 세팅, 가동 및 결과 report 정리를 위한 Repository 입니다.
Window 와 Linux 환경 모두에서 사용 가능합니다.
Installation 및 Usage를 통해 간단한 test가 가능하지만
다중 작업 결과물을 통한 csv file 생성의 경우 약간의 python script 수정이 필요합니다.
# Install Docker in Linux System
sudo wget -qO- http://get.docker.com/ | sh
# 서버 내 도커가 있는 경우 생략# Install Docker in Window
https://www.docker.com/products/docker-desktop/
# Window에서는 도커 데스크탑을 통해 container 관리 및 이미지 확인, 도커 활성화를 시킬 수 있습니다.docker pull pharmai/plip
# Window에서는 Power Shell CMD를 통해 docker 명령어를 실행합니다.- Docker Download 및 PLIP setting에 문제가 있을 경우 Issues 부탁드립니다!
docker run --rm -v ${PWD}:/results -w /r0esults -u $(id -u ${USER}):$(id -g ${USER}) pharmai/plip:latest -f input.pdb -o output_dir_path -x -t -y -p -v
# 해당 명령어를 실행 할 경우
# 저장되어있는 도커 이미지를 통해 input(.pdb file)에서 ouptut을 얻을 수 있습니다.
# 도커 이미지는 해당 명령어가 실행된 뒤 자동으로 종료되며 Docker start, Docker attach로 접근이 불가능합니다.
# -o 옵션에서 지정한 경로 아래
# report.txt
# report.xml
# interaction_image.png
# interaction_pymol_file.pse
# target.pdb
# result_1.pdb
# result_2.pdb
# 등의 output file들이 생성.
# 이 중 report.txt를 통해 상세 interaction score 확인 가능# For get interactions in specific peptide chain
docker run --rm -v ${PWD}:/results -w /r0esults -u $(id -u ${USER}):$(id -g ${USER}) pharmai/plip:latest -f input.pdb -o output_dir_path --peptides A -x -t -y -p -v
# --peptides A : A chain peptide와 단백질간의 결합 예측- 위의 명령어를 정렬하여 하나하나 실행시키는 것이 아닌 다중 작업을 수행할 수 있다.
- Linux에서는 bash script(.sh), Window에서는 powershell script(.ps1) 혹은 python script를 통해 다중작업 수행
# Example file
# [script.ps1] or [script.sh]
docker run --rm -v ${PWD}:/results -w /r0esults -u $(id -u ${USER}):$(id -g ${USER}) pharmai/plip:latest -f input_1.pdb -o output_dir_path/1 -x -t -y -p -v
docker run --rm -v ${PWD}:/results -w /r0esults -u $(id -u ${USER}):$(id -g ${USER}) pharmai/plip:latest -f input_2.pdb -o output_dir_path/2 -x -t -y -p -v
docker run --rm -v ${PWD}:/results -w /r0esults -u $(id -u ${USER}):$(id -g ${USER}) pharmai/plip:latest -f input_3.pdb -o output_dir_path/3 -x -t -y -p -vbash script.sh
bash script.ps1
# power shell에서 script 실행 권한 에러가 발생할 경우 아래 링크 참조
# https://betterinvesting.tistory.com/276time parallel --bar -S10.0.86.{1..100} -j 1 --joblog j --res o --resume-failed --files -a script_file
# Linux 서버가 많을 경우 parallel command를 통해 병렬처리를 하여 작업시간을 단축시킬 수 있습니다.
# 엄청난 대량 작업이 아니라면 Window에서도 충분히 단 시간내에 결과 도출 가능- output.pse
- Interactions : Show Protein-Ligand Interactions to line in pymol
- Structures : Ligand and Target Protein Binding Locations to stick in pymol
- report.txt
Prediction of noncovalent interactions for PDB structure Target_PROTEIN
==============================================================================================
Created on 2023/11/10 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.
UNK:Z:0 (UNK) - SMALLMOLECULE
-----------------------------
Interacting chain(s): A
**Hydrophobic Interactions**
+-------+---------+----------+-----------+-------------+--------------+------+--------------+---------------+------------------------+-----------------------+
| RESNR | RESTYPE | RESCHAIN | RESNR_LIG | RESTYPE_LIG | RESCHAIN_LIG | DIST | LIGCARBONIDX | PROTCARBONIDX | LIGCOO | PROTCOO |
+=======+=========+==========+===========+=============+==============+======+==============+===============+========================+=======================+
| 639 | PRO | A | 0 | UNK | Z | 3.90 | 23 | 3854 | 10.080, 48.240, -0.776 | 11.952, 47.829, 2.621 |
+-------+---------+----------+-----------+-------------+--------------+------+--------------+---------------+------------------------+-----------------------+
**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 |
+=======+=========+==========+===========+=============+==============+===========+==========+==========+===========+===========+==========+===========+=============+==============+========================+========================+
| 613 | SER | A | 0 | UNK | Z | False | 1.64 | 2.61 | 167.72 | True | 3652 | Nam | 31 | O3 | 11.171, 43.877, -0.034 | 11.905, 41.433, 0.514 |
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+
| 613 | SER | A | 0 | UNK | Z | True | 2.00 | 2.66 | 123.43 | True | 3657 | O3 | 66 | O.co2 | 15.688, 45.568, -0.504 | 13.963, 43.566, -0.189 |
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+
| 641 | THR | A | 0 | UNK | Z | True | 3.42 | 3.99 | 119.74 | True | 3874 | O3 | 56 | O.co2 | 14.445, 47.370, 6.481 | 16.597, 47.121, 9.836 |
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+
**Salt Bridges**
+-------+---------+----------+----------------+-----------+-------------+--------------+------+-----------+-----------+-------------------+------------------------+-----------------------+
| RESNR | RESTYPE | RESCHAIN | PROT_IDX_LIST | RESNR_LIG | RESTYPE_LIG | RESCHAIN_LIG | DIST | PROTISPOS | LIG_GROUP | LIG_IDX_LIST | LIGCOO | PROTCOO |
+=======+=========+==========+================+===========+=============+==============+======+===========+===========+===================+========================+=======================+
| 609 | ARG | A | 3622,3624,3625 | 0 | UNK | Z | 4.84 | True | Phosphate | 28,28,27,29,30,31 | 10.198, 45.028, -0.884 | 5.445, 45.662, -0.234 |
+-------+---------+----------+----------------+-----------+-------------+--------------+------+-----------+-----------+-------------------+------------------------+-----------------------+- python script를 통해 생성된 report.txt 내 데이터를 추출하여 csv file 생성
- '-f' or '-i' is a necessary parameter
-h, --help show this help message and exit
-f INPUT [INPUT ...], --file INPUT [INPUT ...]
Set input file, '-' reads from stdin
-i PDBID [PDBID ...], --input PDBID [PDBID ...]
-o OUTPATH, --out OUTPATH
-O, --stdout Write to stdout instead of file
--rawstring Use Python raw strings for stdin
-v, --verbose Turn on verbose mode
-q, --quiet Turn on quiet mode
-s, --silent Turn on silent mode
-p, --pics Additional pictures
-x, --xml Generate report file in XML format
-t, --txt Generate report file in TXT (RST) format
-y, --pymol Additional PyMOL session files
--maxthreads MAXTHREADS
Set maximum number of main threads (number of binding
sites processed simultaneously).If not set, PLIP uses
all available CPUs if possible.
--breakcomposite Don't combine ligand fragments with covalent bonds but
treat them as single ligands for the analysis.
--altlocation Also consider alternate locations for atoms (e.g.
alternate conformations).
--nofix Turns off fixing of PDB files.
--nofixfile Turns off writing files for fixed PDB files.
--nopdbcanmap Turns off calculation of mapping between canonical and
PDB atom order for ligands.
--dnareceptor Treat nucleic acids as part of the receptor structure
(together with any present protein) instead of as a
ligand.
--name OUTPUTFILENAME
Set a filename for the report TXT and XML files. Will
only work when processing single structures.
--peptides PEPTIDES [PEPTIDES ...], --inter PEPTIDES [PEPTIDES ...]
Allows to define one or multiple chains as peptide
ligands or to detect inter-chain contacts
--intra INTRA Allows to define one chain to analyze intra-chain
contacts.
--keepmod Keep modified residues as ligands
--nohydro Do not add polar hydrogens in case your structure
already contains hydrogens.
--model MODEL Model number to be used for multi-model structures.
- 상세한 output report 및 내용을 확인하시려면 Document 참조