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2013 ; 12
(ä): 831-57
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English Wikipedia
A simple click by click protocol to perform docking: AutoDock 4 2 made easy for
non-bioinformaticians
#MMPMID26648810
Rizvi SM
; Shakil S
; Haneef M
EXCLI J
2013[]; 12
(ä): 831-57
PMID26648810
show ga
Recently, bioinformatics has advanced to the level that it allows almost accurate
prediction of molecular interactions that hold together a protein and a ligand in
the bound state. For instance, the program AutoDock has been developed to provide
a procedure for predicting the interaction of small molecules with macromolecular
targets which can easily separate compounds with micromolar and nanomolar binding
constants from those with millimolar binding constants and can often rank
molecules with finer differences in affinity. AutoDock can be used to screen a
variety of possible compounds, searching for new compounds with specific binding
properties or testing a range of modifications of an existing compound. The
present work is a detailed outline of the protocol to use AutoDock in a more
user-friendly manner. The first step is to retrieve required Ligand and
Target.pdb files from major databases. The second step is preparing PDBQT format
files for Target and Ligand (Target.pdbqt, Ligand.pdbqt) and Grid and Docking
Parameter file (a.gpf and a.dpf) using AutoDock 4.2. The third step is to perform
molecular docking using Cygwin and finally the results are analyzed. With due
confidence, this is our humble claim that a researcher with no previous
background in bioinformatics research would be able to perform molecular docking
using AutoDock 4.2 program by following stepwise guidelines given in this
article.