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AUTODOCK Tutorial
Applications required
1. Marvin View
2. AUTODOCK 1.5.6 or 1.5.4
Input files required
1. Ligand in PDB forma ! "igand.#d$
2. %e&e#or in PDB forma ! re&e#or.#d$
Preparing ligand.pdb file
O$ain a "igand 'r(&(re in .MOL or .)D* forma !
O#en we$'ie of Dr(gBan+ ,#-www.dr(g$an+.&a and /#e ,e name
of
de'ired "igand on 'ear&, $ar0 for V31 %ever'e
Tran'&ri#a'e re&e#orevira#ine i' 'e"e&ed a' Ligand.
T,i' wi"" o#en a window from w,ere /o( &an
&"i&+ on MOL or )D* w,i&, wi"" $e di'#"a/ed ('
&o#/ and 'ave a' "igand.
fi"e. f "igand 'r(&(re i' no avai"a$"e in Dr(gBan+ r/ CB or
o,er 'ie'.
Convering )D* or MOL forma o PDB forma
O#en ,e "igand. fi"e wi, Marvin view. C"i&+ )r(&(re from
men( $ar and
&"i&+ C"ean in 2D fo""owed $/ C"ean in 7D0 C"i&+
*i"e on men( $ar and 'e"e&
'ave a"" w,i&, o#en' a new window 'e"e& *i"e' of /#e a'
PDB give ,e fi"e
name a' "igand.#d$ and 'ave.
Convering "igand.#d$ o "igand .#d$8 9:(a"i/ 'r(&(re;O#en
AUTODOCK 1.5.4 ,e "igand. fi"e wi, Marvin view. C"i&+
)r(&(re
from men( $ar and &"i&+ C"ean in 2D fo""owed $/ C"ean in
7D0 C"i&+ *i"e on
men( $ar and 'e"e& 'ave a"" w,i&, o#en' a new window
'e"e& *i"e' of /#e a'
PDB give ,e fi"e name a' "igand.#d$ and 'ave.
Preparing receptor.pdbqt file
O$ain re&e#or 'r(&(re in .PDB forma
O#en %C)B PDB we$'ie ,#-www.r&'$.org#d$,ome,ome.do/#e ,e
name of de'ired #roein in 'ear&, $ar for e.g. (n"iganded V31
%ever'e
Tran'&ri#a'e w,i&, wi"" ',ow re'("' &"i&+ on ,e
re'(" o o#en.
Using Autodock 1.5. or 1.5.!
O#en A(oDo&+ Too"' 1.5.6 and fo""ow ,e 'e8(en&e
Pre#aring Proein
i. *i"eread mo"e&("e'e"e& re&e#or.#d$
ii. De"ee waer mo"e&("e'0 "igand0 '("#,ae'
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iii. @di/drogen'Add
iv. T,i' o#en' a new window 'e"e& Po"ar On"/0 noBond Order
and e'
from i0 ,i' wi"" add #o"ar ,/drogen aom' ,a are im#oran for
Do&+ing.
v. *i"e)ave>rie PDB)aveO+ vi. )ave ,e #re#ared re&e#or a'
re&e#or.#d$
vii. @diDe"eeDe"ee A"" Mo"e&("e'
Pre#aring Ligand 9"igand.#d$8;
i. Ligandn#(O#en"igand.#d$
ii. T,i' wi"" o#en ,e "igand
iii. LigandTor'ion reeDee& %oo
iv. LigandTor'ion ree),ow %oo @#an'ion
v. LigandTor'ion reeC,oo'e Tor'ion' vi. LigandTor'ion ree)e
n(m$er of or'ion'
vii. T,i' 'e' no. of or'ion ang"e' ,a a mo"e&("e &an
,ave d(ring
&onformaion'.
viii. LigandO(#()ave a' PDB:T
i. ow o(r "igand.#d$8 i' read/.
. @diDe"eeDe"ee A"" Mo"e&("e'
Pre#aring re&e#or.#d$8 and rid Parameer *i"e 9.P*;
i. ridMa&romo"e&("ere&e#or.#d$O#en ii. T,i' o#en' ,e
.PDB 'r(&(re of re&e#or and &onver' i o .PDB:T
in'ide ,e 'ame #a,0 name i a' re&e#or.#d$8 and )ave
iii. rid)e Aom /#e'Dire&"/
iv. T,i' wi"" o#en a new window w,ere we need o '#e&if/ ,e
aom' in
"igand0 for genera"iing ,e '(d/ we &an '#e&if/ fo""owing
aom' in
window w,i&, &an $e ('ed for an/ "igand and
&"i&+ A&&e#
A C C" Br * ) P D A OA )A
v. ridrid Bo
vi. T,i' &ommand o#en' a new window w,ere we need o
'#e&if/ ,e 7D'#a&e for do&+ing w,i&, i' &a""ed
%D.
vii. To 'e grid we need o +now ,e amino a&id' of re&e#or
w,i&,
&ommon"/ inera& wi, +nown "igand'. B/ a+ing ,e average
of
E &o3ordinae' of inera&ing amino a&id' we wi"" ener
,e va"(e' in
,i' window.
viii. To o$ain inera&ing amino a&id'
o#en PDB'(m ,#-www.e$i.a&.(+#d$'(m and /#e ,e #d$ &ode
of
"iganded re&e#or in 'ear&, $ar e.g. 2ED1.
2
http://www.ebi.ac.uk/pdbsum/http://www.ebi.ac.uk/pdbsum/
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A(odo&+4 !# "igand.d#f !" "igand.d"g
v. T,i' wi"" &reae "igand.g"g fi"e w,i&, &an $e
vi'(a"ied ('ing A(oDo&+
4
