LightDock：高效蛋白质-DNA对接框架

GitHub - lightdock/lightdock: Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

lightdock - 大分子对接框架_PyPI中文网

蛋白质-DNA 对接 | LightDock --- Protein-DNA Docking | LightDock

先学会后应用~

1.下载安装相关包~

lightdock

pip3 install lightdock -i https://pypi.tuna.tsinghua.edu.cn/simple

git clone https://github.com/lightdock/lightdock.git

cd lightdock
pip install -e .

# LightDock
export LIGHTDOCK_HOME="/path/to/lightdock"
export PATH=$PATH:$LIGHTDOCK_HOME/bin
export PYTHONPATH=$PYTHONPATH:$LIGHTDOCK_HOME

reduce

git clone https://github.com/rlabduke/reduce.git

使用cmake 

mkdir -p ~/build/reduce
cd ~/build/reduce
cmake ~/src/reduce
make
sudo make install

PDB-Tools

Python 包 GitHub - haddocking/pdb-tools: A dependency-free cross-platform swiss army knife for PDB files.

pip install pdb-tools

# To download
git clone https://github.com/haddocking/pdb-tools
cd pdb-tools# To update
git pull origin master# To install
python setup.py install

2.linux run LightDock

以官方示例数据作为演示

• 1. Copying the data

• mkdir data
  cd data
  curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/dna_docking/data/1AZP_A.pdb
  curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/dna_docking/data/1AZP_B.pdb

• 2. Specifying residue restraints

• cd lightdock/lightdock/lightdock/curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/dna_docking/data/restraints.list

• 3. Protonation
  • 3.1. Protein

  • reduce -Trim 1AZP_A.pdb > 1AZP_A_noh.pdb
    reduce -BUILD 1AZP_A_noh.pdb > 1AZP_A_h.pdb

  • pdb_atom_renumber 1AZP_A_h.pdb > protein.pdb Renumbering a structure  重新编号结构pdb_reres -1 1AZP_A_h.pdb > protein.pdb

  • 
    
    3.2. DNA

  • reduce -Trim 1AZP_B.pdb > 1AZP_B_noh.pdb
    reduce -BUILD 1AZP_B_noh.pdb > 1AZP_B_h.pdb

    上传 reduce_to_amber.py 到 lightdock/lightdock/lightdock/ 

  • mv data/1AZP_B_h.pdb  ../lightdock/cd lightdock/lightdock/lightdock/
    python reduce_to_amber.py 1AZP_B_h.pdb dna.pdb

• 4. Setup

• mv data/protein.pdb  ../lightdocklightdock3_setup.py protein.pdb dna.pdb -anm -rst restraints.listlgd_setup.py ./lightdock/protein.pdb ./lightdock/dna.pdb -anm -rst ./lightdock/restraints.list
  

• 
• 5. Simulation

• lightdock3.py setup.json 100 -s dna -c 8lgd_run.py setup.json 100 -s dna -c 8
  

• 6. Clustering and Filtering

• #PBS -N 1AZP-post
  #PBS -q medium
  #PBS -l nodes=1:ppn=8
  #PBS -S /bin/bash
  #PBS -d ./
  #PBS -e ./postprocessing.err
  #PBS -o ./postprocessing.out### Calculate the number of swarms ###
  s=`ls -d ./swarm_* | wc -l`
  swarms=$((s-1))### Create files for Ant-Thony ###for i in $(seq 0 $swarms)doecho "cd swarm_${i}; lgd_generate_conformations.py ../protein.pdb ../dna.pdb  gso_100.out 200 > /dev/null 2> /dev/null;" >> generate_lightdock.list;donefor i in $(seq 0 $swarms)doecho "cd swarm_${i}; lgd_cluster_bsas.py gso_100.out > /dev/null 2> /dev/null;" >> cluster_lightdock.list;done### Generate LightDock models ###
  ant_thony.py -c 8 generate_lightdock.list;### Clustering BSAS (rmsd) within swarm ###
  ant_thony.py -c 8 cluster_lightdock.list;### Generate ranking files for filtering ###
  lgd_rank.py $s 100;### Filtering models by >40% of satisfied restraints ###
  lgd_filter_restraints.py --cutoff 5.0 --fnat 0.4 -lnuc rank_by_scoring.list restraints.list A B
  

  #PBS -N 1AZP-post
  #PBS -q medium
  #PBS -l nodes=1:ppn=8
  #PBS -S /bin/bash
  #PBS -d ./
  #PBS -e ./postprocessing.err
  #PBS -o ./postprocessing.out### Calculate the number of swarms ###
  s=`ls -d ./swarm_* | wc -l`
  swarms=$((s-1))### Create files for Ant-Thony ###
  for i in $(seq 0 $swarms)doecho "cd swarm_${i}; lgd_generate_conformations.py ../protein.pdb ../dna.pdb  gso_100.out 200 > /dev/null 2> /dev/null;" >> generate_lightdock.list;donefor i in $(seq 0 $swarms)doecho "cd swarm_${i}; lgd_cluster_bsas.py gso_100.out > /dev/null 2> /dev/null;" >> cluster_lightdock.list;done### Generate LightDock models ###
  ant_thony.py -c 8 generate_lightdock.list;### Clustering BSAS (rmsd) within swarm ###
  ant_thony.py -c 8 cluster_lightdock.list;### Generate ranking files for filtering ###
  lgd_rank.py $s 100;### Filtering models by >40% of satisfied restraints ###
  lgd_filter_restraints.py --cutoff 5.0 --fnat 0.4 -lnuc rank_by_scoring.list restraints.list A B
  

• ​​dz 

• Renumbering a structure  重新编号结构

  pdb_reres -1 1ctf.pdb > 1ctf_renumbered.pdb

pdb_reres -1 1ctf.pdb > 1ctf_renumbered.pdbpdb_reres -1 1AZP_A_h.pdb > protein.pdb

rm -rf swarm_*

用lightdock 进行Protein-DNA docking prediction。 首先，我们需要确保蛋白质配体的氢原子符合我们在 dna 评分函数中的参数化（ dna 评分函数基于 AMBER94 力场）。为此，我们将使用 reduce 软件。请问如何在Linux系统用conda安装 reduce ？

我们使用 PDB-Tools（网络服务器或 Python 包）重新编号了蛋白质受体配体的原子：

这里用