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Applications Required: AUTODOCK Tutorial

This document provides instructions for using Autodock 1.5.6 or 1.5.4 to perform molecular docking simulations. It describes how to prepare the ligand and receptor files in PDBQT format, generate the grid parameter file, set up the docking parameter file, and run Autogrid and Autodock to perform the docking. Key steps include: 1. Obtaining the ligand and receptor structures in PDB format 2. Preparing the files using Autodock Tools by adding hydrogens, removing water molecules etc. 3. Setting the number of torsions and grid box size 4. Generating the grid map files using Autogrid 5. Setting the docking

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Renjith Raveendran Pillai
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128 views4 pages

Applications Required: AUTODOCK Tutorial

This document provides instructions for using Autodock 1.5.6 or 1.5.4 to perform molecular docking simulations. It describes how to prepare the ligand and receptor files in PDBQT format, generate the grid parameter file, set up the docking parameter file, and run Autogrid and Autodock to perform the docking. Key steps include: 1. Obtaining the ligand and receptor structures in PDB format 2. Preparing the files using Autodock Tools by adding hydrogens, removing water molecules etc. 3. Setting the number of torsions and grid box size 4. Generating the grid map files using Autogrid 5. Setting the docking

Uploaded by

Renjith Raveendran Pillai
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOC, PDF, TXT or read online on Scribd
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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 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

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