Docking is a widely used method in the medicinal chemistry area there are more than 50 docking algorithms or software out there, some of them are more commercial while some others are more academic. Here what I presented here is a more academic one derived from the famous Auto Dock, called Smina. This protocol utilizes a lot of readily available free packages like Pymol, py3Dmol, etc, to provide you a FREE docking option, in a programmatical manner.

The docking codes are borrowed from other sources https://www.cheminformania.com/ligand-docking-with-smina/, but overall, the whole procedure is integrated by myself, especially when it comes to the method of Minicoda installation, I restrict it to python3.7, otherwise, if we install the latest one, it is very likely we will encounter incompatible issues when trying to install Rdkt and Openbabel.

Happy modeling!

! wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh
! chmod +x Miniconda3-py37_4.8.2-Linux-x86_64.sh
! bash ./Miniconda3-py37_4.8.2-Linux-x86_64.sh -b -f -p /usr/local
! conda install -c rdkit rdkit -y
import sys
sys.path.append('/usr/local/lib/python3.7/site-packages/')

!time conda install -q -y -c openbabel openbabel

import sys
sys.path.append('/usr/local/lib/python3.7/site-packages/')

!pip install py3Dmol # 3D Molecular Visualizer

Requirement already satisfied: py3Dmol in /usr/local/lib/python3.7/site-packages (0.9.1)

import os
import numpy as np
from sklearn.ensemble import RandomForestClassifier
from sklearn.model_selection import StratifiedKFold
from sklearn.metrics import accuracy_score
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import DataStructs
from rdkit.Chem import RDConfig
from rdkit.Chem import rdBase
import pickle
from sklearn.metrics import classification_report, confusion_matrix, accuracy_score
print(rdBase.rdkitVersion)

!wget https://sourceforge.net/projects/smina/files/smina.static/download -O smina.static

!chmod u+x smina.static

!./smina.static

! apt-get install pymol 

!wget -O 1OYT.pdb https://files.rcsb.org/download/1oyt.pdb
com_file = open('fetch_and_clean.pml','w')
com_file.write('''
load 1OYT.pdb
remove resn HOH
h_add elem O or elem N
select 1OYT-FSN, resn FSN #Create a selection called 1OYT-FSN from the ligand
select 1OYT-receptor, 1OYT and not 1OYT-FSN #Select all that is not the ligand
save 1OYT-FSN.pdb, 1OYT-FSN
save 1OYT-receptor.pdb, 1OYT-receptor    
''')
com_file.close()

!pymol -c fetch_and_clean.pml

!obabel 1OYT-receptor.pdb -xr -O 1OYT-receptor.pdbqt
!obabel 1OYT-FSN.pdb -O 1OYT-FSN.pdbqt

!./smina.static -r 1OYT-receptor.pdbqt -l 1OYT-FSN.pdbqt --autobox_ligand 1OYT-FSN.pdbqt --autobox_add 8 --exhaustiveness 16 -o 1OYT-redock.pdbqt

import py3Dmol

def drawit2(m,confId=-1):
    mb = Chem.MolToMolBlock(m,confId=confId)
    p = py3Dmol.view(width=400, height=400)
    p.addModel(mb,'sdf')
    p.setStyle({'stick':{}})
    p.setBackgroundColor('0xeeeeee')
    p.zoomTo()
    return p

def DrawComplex(protein,ligand):
    complex_pl = Chem.MolToPDBBlock(Chem.CombineMols(protein,ligand))
    #complex_mol=Chem.CombineMols(receptor,mols[-1])
    view = py3Dmol.view(width=600,height=600)
    view.addModel(complex_pl,'pdb')
    #view.addModel(Chem.MolToMolBlock(mols[0]),'sdf')
    chA = {'chain':['H','L','I']}
    chB = {'resn':'UNL'}
    view.setStyle(chA,{'cartoon': {'color':'spectrum'}})
    #view.setStyle(chA,{'lines': {}})
    view.addSurface(py3Dmol.VDW,{'opacity':0.8}, chB)
    view.setStyle(chB,{'stick':{}})
    view.zoomTo()
    return view   

from rdkit import Chem

!obabel 1OYT-redock.pdbqt -O 1OYT-redocked.sdf

9 molecules converted

mols = [m for m in Chem.SDMolSupplier('1OYT-redocked.sdf') if m is not None]

drawit2(mols[8])

receptor = Chem.MolFromPDBFile('1OYT-receptor.pdb')
DrawComplex(receptor,mols[8])