PLIP–蛋白质-配体相互作用分析
安装
Docker方式
#install Docker (https://docs.docker.com/engine/install/centos/) and plip
sudo yum remove docker \
docker-client \
docker-client-latest \
docker-common \
docker-latest \
docker-latest-logrotate \
docker-logrotate \
docker-engine
sudo yum-config-manager \
--add-repo \
https://download.docker.com/linux/centos/docker-ce.repo
sudo yum install docker-ce docker-ce-cli containerd.io
#启动Docker服务
sudo systemctl start docker
#把用户shouli加到Docker组
sudo usermod shouli -a -G docker && bash
#从Docker源拉PLIP镜像
docker pull pharmai/plip:latest
#use PLIP 处理5c8k.pdb复合物文件,-v是将PLIP计算的结果传到我们现在的地址(${PWD})
docker run --rm -v ${
PWD}:/results -w /results pharmai/plip:latest -f 5c8k.pdb -yv -t --name 5c8k_output
Python源码方式
# Install Dependicies
cd ~/software
wget -c https://github.com/openbabel/openbabel/archive/refs/tags/openbabel-3-1-1.tar.gz
tar -zxvf openbabel-3-1-1.tar.gz
mkdir build
cd build
cmake .. -DPYTHON_BINDINGS=ON -DCMAKE_INSTALL_PREFIX=~/software/openbabel
make
make install
pip install plip
## 使用
plip -i 1osn -pyx
参数
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]
The Protein-Ligand Interaction Profiler (PLIP) 2.1.0-betais a command-line
based tool to analyze interactions in a protein-ligand complex. If you are
using PLIP in your work, please cite: Salentin,S. et al. PLIP: fully automated
protein-ligand interaction profiler. Nucl. Acids Res. (1 July 2015) 43 (W1):
W443-W447. doi:10.1093/nar/gkv315Supported and maintained by: PharmAI GmbH
(2020) - www.pharm.ai - hello@pharm.ai
optional arguments:
-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 stdout and stdin
-v, --verbose Turn on verbose mode
-q, --quiet Turn on quiet mode
-s, --silent Turn on silent mode
-p, --pics Additional pictures #添加渲染图片
-x, --xml Generate report file in XML format # 添加XML结果报告文件
-t, --txt Generate report file in TXT (RST) format # 添加TXT结果报告文件
-y, --pymol Additional PyMOL session files # 附加的PyMOL会话文件
--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 Uses the DNA instead of the protein as a receptor for
interactions.
--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.
参考
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