Docking molecules with Vina
Autodock Vina
To study molecules they must be
docked
• Docked molecules bind their enzyme or
receptor in a specific conformation
• Docked molecules bind with high affinity
• The best way to get docked conformation is to
use X-ray crystallography
• Alternative: use docking software like Vina to
predict docked conformation
What is docking?
• Find the conformation with which a ligand
binds a receptor
• This information includes full coordinates of
all ligand atoms
• The docked configuration is the (presumed)
lowest energy binding site
Steps
• 1. get protein structure
• 2. create files with protein only
• 3. Use a known ligand (not your ligand) to
define the ligand binding site
• 4. Generate some modified structure files
• 5. Use files with docking software
• 6. Extract predicted conformation and make
new file with protein and target ligand docked
Make a folder
• Need a place to store many files
• Make c:\thesis
Get PDB file
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Go to PDB RSCB on web
Search for PDB code if unknown
Once PDB code is known, download it
Use PDB/Tools, download entries and follow
instructions
You must have Java enabled
Change mmCIF to PDB as type of file
Change compressed to uncompressed
Save in your thesis folder
PDB search
PDB download
PDB info – Protein name
PDB – ligand name (HET)
PDB coordinates
Start with PDB file with protein and
ligand (not your ligand)
• Make a copy of the PDB file
• Split it into only protein and only ligand
• Ligand will be used to get coordinates of
binding site
• Example: beta adrenergic receptor and
carazolol
• 2rh1.pdb
Use wordpad text editor
• Copy cau (= carazolol, ligand) from 2rh1
• Paste into a file called car.pdb
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REMARK carazolol
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HETATM
HETATM
HETATM
HETATM
HETATM
3598
3599
3600
3601
3602
O17
C16
C18
N19
C20
CAU
CAU
CAU
CAU
CAU
A
A
A
A
A
408
408
408
408
408
-33.477
-32.267
-32.478
-33.702
-33.806
10.957
10.230
8.951
8.250
6.805
8.170
8.041
7.225
7.600
7.498
1.00
1.00
1.00
1.00
1.00
50.96
45.65
51.24
54.99
60.13
O
C
C
N
C
PDB files have 3D structure
information including XYZ coordinates
of atoms
• Also have atom numbers
• Residue numbers
• Atom types
Find the center of the ligand
• This will be the center used when you dock
your ligand to the receptor
• Start with the X coordinate. Add all the X
values and then divide by the number of
atoms. Record for later
• Repeat for Y and Z coordinates
• The only purpose of having a ligand at this
point is to define the ligand binding site.
Find coordinates
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z
y
x
REMARK carazolol
HETATM 3598 O17 CAU A 408 -33.477 10.957 8.170 1.00 50.96
HETATM 3599 C16 CAU A 408 -32.267 10.230 8.041 1.00 45.65
HETATM 3600 C18 CAU A 408 -32.478 8.951 7.225 1.00 51.24
HETATM 3601 N19 CAU A 408 -33.702 8.250 7.600 1.00 54.99
HETATM 3602 C20 CAU A 408 -33.806 6.805 7.498 1.00 60.13
O
C
C
N
C
Carazolol – no hydrogens
Visualizing structures
• Try rasmol or raswin
• Download at google: rasmol bernstein
• Several web tutorials available
Adding hydrogens
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Hydrogen is rarely found in PDB files
But all atoms are needed to dock molecules
Solution: add back missing hydrogens
We will use Babel
OpenBabel
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Download openbabel from its web site
Install
Use the command prompt to run the program
Use a full ‘path’, that is a description of the
program location
• Add hydrogens
• On my machine that is (one line):
• \lm\downloads\openbabel-2.1.1\babel.exe
-ipdb car.pdb –opdb carH.pdb -h
Add H
Check that hydrogens have been
added
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HETATM
HETATM
HETATM
ATOM
ATOM
ATOM
20
21
22
23
24
25
C1
C6
C5
H
H
H
CAU
CAU
CAU
CAU
CAU
CAU
408
408
408
408
408
408
-26.395
-27.717
-28.269
-34.319
-31.904
-31.591
6.432
6.731
7.948
10.255
9.929
8.256
7.689
8.006
7.652
8.260
9.079
7.396
1.00
1.00
1.00
1.00
1.00
1.00
0.00
0.00
0.00
0.00
0.00
0.00
C
C
C
H
H
H
Other ligands
• Up to now we have been dealing with the
ligand found in the PDB file with your
receptor/protein
• You may wish to try docking that ligand as a
control
• At some point you will want to deal with other
ligands
Getting other ligands
• To use ligands they must be transferred from
the page to PDB format
• Some ligands may be present in other files in
the protein data bank – try searching
• Ligands can be drawn, e.g. with DS Viewer Pro
or other software and saved in PDB format
• Most ligand files will have to have hydrogens
added
Add hydrogen to the protein
• Repeat ligand procedure, but with protein
• We did car.pdb  carH.pdb
• Now make copy of the protein pdb file with
the ligand deleted (e.g. CAU in this example)
• (you can delete WAT and other ligands too)
• Now, with full path, use babel to add H
Add hydrogen to protein
• Full path on my machine (yours will differ)
• \lm\downloads\babel-2.1.1\babel.exe –ipdb
bar.pdb –opdb barH.pdb -h
• Result: bar.pdb  barH.pdb
We’re almost ready to dock
• But we need two things:
• Torsions
• Hydrogen bonds
Torsions
• The ligand may have rotatable bonds
• Benzene can not twist (0 torsions)
• Hexane can twist (3 torsions, we’ll ignore
rotating methyl groups)
• MGLtools calculates these
• Vina will twist the ligand to try to find the best
fit during docking
H bonds
• We need to find H bond acceptors and donors
• MGLtools also calculates these
MGLtools
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MGLtool, ADT, Autodock tools are the same
Download from MGLtools site
Install
Read tutorial
Click to open window
MGLtools
MGLtools
We will use MGLtools/Autodock tools for two
things:
Annotate the ligand(s)
Annotate the receptor
Autodock / MGL tools
• First we will process the ligand to add torsions
and H bond information
• On left side of ADT screen find ligand menu
• Open ligandH.pdb (or other file)
• Note: this is the ligand file you want to dock,
not the X-yl structure file, unless you are
docking it as a control
Autodock/MGLtools and ligand
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Select torsion tree
Find the ligand torsion ‘root’. Detect root
Aromatic carbons: set names
Output: Save file as carH.pdbqt
It is key that you save the pdbqt file that
MGLtools makes
ADT and protein/receptor
• Find ‘grid’ menu
• Macromolecule
• Open receptor file with hydrogens
(receptorH.pdb)
• The file gets processed
• Save as ligandH.pdbqt
• Do not choose ‘flexible’
ADT receptor refinement
• Now the receptor file and ligand file have
been saved as .pdbqt files.
• These have H bond and torsion information
• Look at the ligandH.pdbqt file using wordpad
or simpletext
• It still looks like a .pdb file, but has extra
information added
Now we have all of the files that we
need to dock a ligand
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Let’s check:
receptorH.pdbqt
ligandH.pdbqt
Binding site coordinates
Setting up Vina
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Vina needs to know what you want to do:
What receptor
What ligand
Where the binding site is
Where to send out the results
This information is placed in a file called
config.txt
Configuration file, config.txt
• Config.txt gives information to Vina as it docks
your ligand
• The left side of each = is Vina code (don’t
change)
• The right side of each = is your input
• You control the site of binding, the size of the
site, and the receptor and ligand
Example Vina configuration file
out = out_carh.pdbqt
receptor = 2rhe.pdbqt
ligand = carh.pdbqt
center_x = -28
center_y = 9
center_z = 6
size_x = 25
size_y = 25
size_z = 25
energy_range = 4
Download Vina
• Web site AutoDock Vina
• Install in ‘thesis’ folder, or wherever your
config file and .pdbqt files are saved.
• Get the right version of Vina for your
computer (e.g. PC vs. Mac)
Autodock Vina
Read manual!
Dock ligand
• Open command prompt
• Make certain that command prompt is
pointed to thesis directory/folder
• Use the cd command with command prompt
or Mac command screen
Finding the right directory
• If necessary change directory using ‘cd’
• E.g. type ‘cd \thesis’ [without the quotes] for
a PC
• Or type ‘cd /thesis’ [without quotes] for mac
• This assumes that you put all your files in the
directory ‘thesis’ on the c:drive or equivalent
• Type dir/p [PC] or ls [Mac] to check that your
files are present
Vina docking
To dock, type :
vina.exe --config config.txt
Vina docking
Vina output
• It takes a minute or two for Vina to dock
• This represents millions of docked positions
being analyzed
• The output file name is defined by the config
file out = outfilename.txt
• Each outfile has several models
• We usually only care about model 1, the best
Output score
• We often want to know how tightly a ligand
binds
• Vina gives an estimate in the output file
• Look for Vina Result: x
• If x is -10 or less, binding is very tight
• If x is -6 to -7 binding is just random, not tight
• In between is hard to judge
Visualizing a docking
• The easiest way is to splice the best ligand
model onto the receptor with its ligand
removed
• Open the outfilename.txt (whatever you
called it in config.txt) – the Vina output
• Copy from the beginning of model 1 to model
2 [note the residue number of the ligand]
• Paste into a copy of the receptor pdb file with
the old ligand removed
Seeing is believing
• Now you can open your new file with receptor
and docked ligand using RasWin or another
visualization program
• Use the residue number of the ligand to select
it (e.g. select 480)
• Convert to spacefill (e.g. spacefill)
• How does it look? Is it in a binding pocked?
Next steps
• Having a ligand binding model is valuable
• Specific contacts can be analyzed
• By comparing two or more models and the
contacts that they make, patterns of receptor
change can be determined
• E.g differences between active and inactive
receptors or receptor subtypes can be
understood