MOE docking instructions and tips, medicinal chemistry and drug design

1. Menna Abdelshaheed

2. I add 3 molecules from MOE to
the same
database
for example ligand ✗ e ligand y e
co -
crystallised ligand . .
.
① Open ☒ ,
Draw ligand ✗
,
Some
in your
folder with name close window .
.
② open new MOFO ,
Draw ligand y ,
save
in
your
folder with name
close window .
Menna Abdelshaheed

3. ③ To isolate co -
crystallized ligand
open
the proteins in THOS ligand
File → Save → in
your
folder with name
e-
g.
co -
crystallized
7K¥se
→ ② only
selected My=mp
Now
we have 3 files containing
the} ligands
II add them
in a database
open any
File of them the
→
@ →
eg× Database
Menna Abdelshaheed

4. Menna AbdElShaheed
Save the database → Folders name .
An empty database
will
appear
the first molecule
will be
added
close
open
ligand Y
from
your
folders open
the database E
→ @→ entry
Now I have
2 molecules
close file of ligand Y
then
Menna Abdelshaheed

5. Open file of co -
cyst. ligand e
open
the database
→
@→
entry
Now I have
the 3 molecules in
my
database
.
y
To prepare
them
compute
→ Molecule
→
wash
~ →
~
→
Partial charges
~ →
~
→ Energy
Minimization
Menna Abdelshaheed

6. After preparation saving
file → Save
as →
Save in your
folder
as
prepared
database
t
Menna Abdelshaheed

7. to change style of a
molecule
0.*
to change
color e
display
if you
want changes
to be on carb@ ⑧ ⇐
Menna Abdelshaheed

8. Molecules drawn in Chandran
file → save →
Folder enamel type
d.
You can open
them in MOE,
I save them in a
database
as
well .
?⃝e op@→ the file ( DIII)
on it
then → Bro@tosaveitas.mdb
④ choose folders
name the
database
Menna Abdelshaheed

9. The database
has the molecules
but not prepared → prepare
them
nole@
↳ ① wash
② partial
charges
Minimal,
Then
the prepared database ③ Energy
☒
→
Folder e name
Menna Abdelshaheed

10. Menna AbdElShaheed
Pro-life →
from s⑤
I can see
number
of chains
if A ←
aa of Ethan A
A) still one
A ←
ligand of chain
chain
A ←
Holt of chain
A
if AA
A
pg
]
2 chains
Menna Abdelshaheed

11. from SE⑨
•
you
can know
the no.
of aa in a certain
☐
chain
→_→
scroll to the
last no .
•
T
o select amino
acids
just
click on them ⇐ Ctrl ) to add more
selection
To do a
certain
function right
click
on any
selected aa
Menna Abdelshaheed

12. e. g.
To hide or show atoms of
certain aa
. s or
color
then
select them → Right
click → Atoms
L
§h@)
hide )
co@
Menna Abdelshaheed

13. preparation
of protein
to-do
To see
if
water
is
needed
won't be removed
from SED if not needed then z
SED
→
Select
water
molecules
( doubleclick
) then right
click
d
n-st.PT
←
↳
②correct → ③ Protnnte
3D
⑧ Minimize ⑦ Save Prepared ptn
Menna Abdelshaheed

14. T
o Make docking in a certain site
of the protein
a-3rd - - et
Most
ii.and ÷
largest
?⃝ site d
site
6 Finder
as it is ✓
go
to site choice
go to site
finder
-10 No
Finder To
choose
the of
choose largest site g. the site
in side co -
cryst.
ligand
>
Menna Abdelshaheed

15. Menna AbdElShaheed
Most suitable site =
Binding site
( active
site)
which already contain the co -
crystalline
ligand -
T
o search for if you
better first select
the ligand e
color it to be able to see
it then open
site finder e go
between
sites until you
find the one having the
ligand .
Menna Abdelshaheed

16. →si-Ap⑤
After choosing
sites ( largest or most
suitable
)
you
make
Isolation
IÑ@ atomseBackbonef-
after isolation
the ligand disappears
you
can
show
it from
show
ligand
To create
Bunnies
click on D€T Created c
• • • • • •
↳
App
Menna Abdelshaheed

17. Docking
① Browse
choose folder
"
"
?⃝¥
a-
Receptor
atoms
or
receptor
+
solvent
if Holt
retained
-
lieand sit Dummy atoms ←
Must be
made
first by
site
finder
Menna Abdelshaheed

18. Menna AbdElShaheed
ligand
✓
m☐B
atoms
#
☒¥@
L
Bug
£
R%
,
'
④ Choose the file
of your
prepared Repair
Tots
database .
¥
Menna Abdelshaheed

19. Docking results must be sorted
at first ③ sort ascending
then saved
File
Save an
choose folder
l name
verging
LL
☐ selected fields only
iG☐ selected E-r.am
Menna Abdelshaheed

20. Scire
as bbb⑤→
Best pose
as lowest energy
→ means
highest
stability e Best
fitting e binding between
the ligand e receptor . .
.
-
10
-
g
→
-200 Best score
- 12
- 20
Menna Abdelshaheed

21. To get
a
picture ④ or
☒
of Best pose
.
Now I
have the results
sorted ascending
so the
best pose ins
no ①
→
Bronc -@
- he
☐
pose
appears
Menna Abdelshaheed

22. Go to
→
ligandinteact.org
(Receptor
atoms]
or Receptor
+ solvent
→
if Holt retained
↳ Browseratmf-imi.cn
then Ap④
2D pic
Export JPG
white
Browse →
folder
→ Name
Menna Abdelshaheed

23. From the Same of 2D interactions
T
e to get a 3D Pic
To hide dummies
RHs☐→Dum①
To create
surface
RH①
→ surf@ →
Snrf
Maps
choose color e. g.
atom
color
or Ñtie2PÉ
Menna Abdelshaheed

24. Menna AbdElShaheed
T
o save 3D pic .
- -
>
file →
Save →
Name
the picture
• save Picture ←
•
Format ⑧
④ You can 9 quality to 100
e 6 resolution
⑤
Menna Abdelshaheed

25. Menna AbdElShaheed
Validation ligand already prepared
←
* Prepare
the protein
/
inside
it.
*
→ ☐o@
→
t.IE
Site : ligand atoms
ligand : ligand atoms
RUNG →
results of docking
←
④ → sang
chelated → ☐ selected only
Menna Abdelshaheed

26. Results of validation
*
value
should be < 1.5
if the software is
valid
which means
deviation from
original docking
is
minimal .
Menna Abdelshaheed