PLIP–蛋白质-配体相互作用分析

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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 -  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