AutoDock分子对接实战

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For this tutorial, the ADFR software suite, providing a number of software tools for automated docking and peripheral tasks, and the Python package meeko, for preparing ligands for example, are necessary.

Meeko

to prepare the ligand

mamba create -n dock python=3.9
mamba activate dock
mamba install -c conda-forge numpy swig boost-cpp sphinx sphinx_rtd_theme openbabel scipy rdkit
pip install meeko

ADFR software suite

https://ccsb.scripps.edu/adfr/downloads/

to prepare receptors

mkdir -p ~/APP/ADFR && cd ~/APP/ADFR
wget https://ccsb.scripps.edu/adfr/download/1038/
tar -xf index.html && cd ADFRsuite_x86_64Linux_1.0
./install.sh -d ~/APP/ADFR -c 0

Vina

https://github.com/ccsb-scripps/AutoDock-Vina/releases

cd ~/APP
wget https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.3/vina_1.2.3_linux_x86_64

download Recptors from Uniport

download the Ligand from PubChem

one Ligand to multiple Recptors

#!/usr/bin/bash
#dock.sh

HOME_DIR=${HOME}/Project/dock
LIGAND_FILE=${HOME_DIR}/L_Aspirin.pdbqt

mk_prepare_ligand=${HOME}/mambaforge/envs/dock/bin/mk_prepare_ligand.py
VINA=${HOME}/APP/vina_1.2.3_linux_x86_64
prepare_receptor=${HOME}/APP/ADFR/bin/prepare_receptor
autogrid=${HOME}/APP/ADFR/bin/autogrid4
pythonsh=${HOME}/APP/ADFR/bin/pythonsh
prepare_gpf=${HOME_DIR}/prepare_gpf.py
N_JOBS=16

cd $HOME_DIR

if  [ ! -d dock_results ]
then
    mkdir dock_results
fi

# 1.Preparing the ligand
$mk_prepare_ligand -i Aspirin.sdf -o $LIGAND_FILE

ls ${HOME_DIR}/*pdb | while read i
do
    RNAME=`basename -s .pdb $i`
    echo $RNAME

    # 2.Preparing the receptor
    $prepare_receptor -r ${RNAME}.pdb -o R_${RNAME}.pdbqt -U waters -A hydrogens
    # 3.Generating affinity maps for AutoDock FF
    $pythonsh $prepare_gpf -l $LIGAND_FILE -r R_${RNAME}.pdbqt -o ${RNAME}.gpf -y
    $autogrid -p ${RNAME}.gpf -l ${RNAME}.glg

    # 4.Running AutoDock Vina
    $VINA \
    --ligand $LIGAND_FILE \
    --maps R_${RNAME} \
    --scoring ad4 \
    --exhaustiveness 32 \
    --out ${HOME_DIR}/dock_results/D_${RNAME}.pdbqt \
    --cpu $N_JOBS \
    --seed 1314

done

bash dock.sh &> dock.log &

files

├── Aspirin.sdf
├── dock.log
├── dock_results
│   └── D_RB1.pdbqt
├── dock.sh
├── L_Aspirin.pdbqt
├── prepare_gpf.py
├── RB1.glg
├── RB1.gpf
├── RB1.pdb
├── R_RB1.A.map
├── R_RB1.C.map
├── R_RB1.d.map
├── R_RB1.e.map
├── R_RB1.HD.map
├── R_RB1.maps.fld
├── R_RB1.maps.xyz
├── R_RB1.OA.map
└── R_RB1.pdbqt

logs

RB1
adding gasteiger charges to peptide
AutoDock Vina v1.2.3
#################################################################
# If you used AutoDock Vina in your work, please cite:          #
#                                                               #
# J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli  #
# AutoDock Vina 1.2.0: New Docking Methods, Expanded Force      #
# Field, and Python Bindings, J. Chem. Inf. Model. (2021)       #
# DOI 10.1021/acs.jcim.1c00203
                                     #
#                                                               #
# O. Trott, A. J. Olson,                                        #
# AutoDock Vina: improving the speed and accuracy of docking    #
# with a new scoring function, efficient optimization and       #
# multithreading, J. Comp. Chem. (2010)                         #
# DOI 10.1002/jcc.21334
                                            #
#                                                               #
# Please see https://github.com/ccsb-scripps/AutoDock-Vina for  #
# more information.                                             #
#################################################################

Scoring function : ad4
Ligand: ~/Project/dock/L_Aspirin.pdbqt
Exhaustiveness: 32
CPU: 16
Verbosity: 1

Reading AD4.2 maps ... done.
Performing docking (random seed: 1314) ... 
0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************

mode |   affinity | dist from best mode
     | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
   1        1.193          0          0
   2        1.193      4.266      5.076
   3        1.193      3.877      4.824
   4        1.193      3.797      4.769
   5        1.193      2.723      4.587
   6        1.193      3.084      4.881
   7        1.193       2.81      4.647
   8        1.193      4.667        5.5
   9        1.193      6.878      8.045

Reference

https://www.chemdraw.com.cn/ruheshiyong/gouxing-youhua.html
https://autodock-vina.readthedocs.io/en/latest/docking_basic.html
https://github.com/ccsb-scripps/AutoDock-Vina/releases