PLIP--蛋白质-配体相互作用分析

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 - [email protected]

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