Applications Required: AUTODOCK Tutorial
Applications Required: 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 12V31 %ever'e Tran'&ri#a'e re&e#or
4evira#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"" $e di'#"a/ed 5(' &o#/ and 'ave a' "igand.6
fi"e. 2f "igand 'r(&(re i' no avai"a$"e in Dr(gBan+ r/ 4CB2 or o,er 'ie'.
Convering )D* or MOL forma o PDB forma
O#en ,e "igand.6 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.6 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&, $ar for e.g. (n"iganded 12V31 %ever'e
Tran'&ri#a'e w,i&, wi"" ',ow re'("' &"i&+ on ,e re'(" o o#en.
Using Autodock 1.5. or 1.5.!
O#en A(oDo&+ Too"' 1.5.6 and fo""ow ,e 'e8(en&e
Pre#aring Proein
i. *i"e read mo"e&("e 'e"e& re&e#or.#d$
ii. De"ee waer mo"e&("e'0 "igand0 '("#,ae' <)O
4
=0 #,o'#,ae' <PO
4
=0
'o"ven'0 'a"' e& ,a are no needed for do&+ing. >e need #(re
re&e#or 'r(&(re for Do&+ing. Lef ,and &on'o"e form *ig ? i' ('ed for
,i'.
1
iii. @di 1/drogen' Add
iv. T,i' o#en' a new window 'e"e& Po"ar On"/0 noBond Order and Ae'
from i0 ,i' wi"" add #o"ar ,/drogen aom' ,a are im#oran for
Do&+ing.
v. *i"e )ave >rie PDB )ave O+
vi. )ave ,e #re#ared re&e#or a' re&e#or1.#d$
vii. @di De"ee De"ee A"" Mo"e&("e'
Pre#aring Ligand 9"igand.#d$8;
i. Ligand 2n#( O#en "igand.#d$
ii. T,i' wi"" o#en ,e "igand
iii. Ligand Tor'ion ree Dee& %oo
iv. Ligand Tor'ion ree ),ow %oo @6#an'ion
v. Ligand Tor'ion ree C,oo'e Tor'ion'
vi. Ligand Tor'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. Ligand O(#( )ave a' PDB:T
i6. 4ow o(r "igand.#d$8 i' read/.
6. @di De"ee De"ee A"" Mo"e&("e'
Pre#aring re&e#or.#d$8 and Brid Parameer *i"e 9.BP*;
i. Brid Ma&romo"e&("e re&e#or1.#d$ 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. Brid )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"iCing ,e '(d/ we &an '#e&if/ fo""owing aom' in
window w,i&, &an $e ('ed for an/ "igand and &"i&+ A&&e#
A C 1 C" Br 2 * ) P 1D 4 4A OA )A
v. Brid Brid Bo6
vi. T,i' &ommand o#en' a new window w,ere we need o '#e&if/ ,e 7D
'#a&e for do&+ing w,i&, i' &a""ed B%2D.
vii. To 'e grid we need o +now ,e amino a&id' of re&e#or w,i&,
&ommon"/ inera& wi, +nown "igand'. B/ a+ing ,e average of
DAE &o3ordinae' of inera&ing amino a&id' we wi"" ener ,e va"(e' in
,i' window.
viii. To o$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&, $ar e.g. 2ED1.
2
i6. A new window i' di'#"a/ed 9*ig 12; &"i&+ on "igand name0 a new window
wi, "igand and inera&ing amino a&id from re&e#or i' o#ened noe down ,e
name'. Ao( &an 'ave ,e "ig#"o in PDf forma.
6. To o$ain DAE &o3ordinae' o#en re&e#or.#d$8 wi, word#ad and
'ear&, for individ(a" aom &o3ordinae'0 add ,em and a+e average.
*or 12V31 rever'e ran'&ri#a'e 911MV; ,e Brid i' &a"&("aed a'
fo""ow'
6i. T,e no. of #oin' in D0 A and E &o3ordinae' are 'e o 6F
in mo' of ,e '(die'.
6ii. 2n grid o#ion' window Cener Pi&+ an aom
T,i' &ommand wi"" #i&+ a &enre and ad5(' ,e grid a&&ording"/.
6iii. 2n 'ame window *i"e C"o'e 'aving &(rren
C"o'e' ,e window and re(rn' o A(oDo&+ window.
6iv. Brid o(#( )ave BP* re&e#or.g#f )ave
Creae' ,e re&e#or.g#f w,i&, i' needed for do&+ing.
6v. Brid @di BP* &an $e ('ed o &,ange grid &enre and &o3ordinae
va"(e' o ineger'. C"i&+ O+
G
Pre#aring Do&+ing Parameer *i"e 9.DP*;
i. Do&+ing Ma&romo"e&("e 'e rigid fi"ename re&e#or.#d$8
ii. Do&+ing Ligand O#en "igand.#d$8
iii. Do&+ing )ear&, Parameer' Benei& A"gori,m
iv. A window a##ear' ma+e '(re o 'e 4o. of BA r(n' o 1F and
#o#("aion )iCe o 15F0 C"i&+ A&&e#.
v. T,ere are o,er )ear&, #arameer' "i+e )im("aed Annea"ing and Lo&a"
)ear&, #arameer' $( Benei& A"gori,m i' mo' effi&ien of ,em a"".
vi. Do&+ing Do&+ing Parameer'
vii. )e a"" ,e #arameer' o U'er Defa("' and &"i&+ A&&e#
viii. Do&+ing O(#( Lamar&+ian BA "igand.d#f )ave
i6. Li+e )ear&, Parameer' ,ere are o#ion' in O(#( "i+e Benei&
A"gori,m0 )im("aed Annea"ing0 Lo&a" )ear&, $( Lamar&+ian BA i'
,e mo' effi&ien of ,em.
6. T,i' .DP* fi"e &onain' #arameer' for Do&+ing.
Docking
i. A"" ,e re8(ired fi"e' 9re&e#or.#d$80 "igand.#d$80 re&e#or.g#f0 "igand.d#f;
',o("d $e 'ored in one fo"der.
ii. O#en &ommand #rom# and &,ange dire&or/ o ,e a$ove menioned fo"der
iii. *ir' r(n ,e Brid fi"e $/ &ommand
A(ogrid4 !# re&e#or.g#f !" re&e#or.g"g
iv. T,en r(n Do&+ing fi"e $/ &ommand
3
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"iCed ('ing A(oDo&+
4