Biomedical Engineering Reference
In-Depth Information
Table 12.1
Wid
ely used docking algorithms
Name
URL
Short summary
AutoDock
Free software of automated small-molecules
docking tools (rigid receptor, flexible
ligand)
DOCK
Free software, small molecules-various
receptor docking (protein, DNA, and
RNA), protein-protein interaction
FlexX
Fast computer program for predicting
protein-ligand interactions
GOLD
Calculating the docking modes of small
molecules in protein binding sites
Glide
Fast flexible ligand docking program (small
molecule-protein)
ICM
Automatic incorporation of fl exibility into
the ligand and receptor docking
(protein, DNA, and RNA), protein-
protein interaction
MORDOR
Docking program using algorithm
considering flexibility of both nucleic
acid receptor and ligand
Sur fl ex-Dock
“Protomol”-guided fl exible molecular
docking program
The docking process concerns the prediction of ligand conformation and orientation
within a targeted binding site (active site) (Kitchen et al.
2004
). In order to carry out
docking calculations, it is necessary to know the 3-dimensional (3D) structure of a
target and the nature of the binding site. 3D structures are identified by X-ray crys-
tallography or NMR experiments and can be downloaded from Protein Data Bank
(PDB) (Berman et al.
2000
) or predicted by homology modeling using various pro-
grams. The next step is to define the binding site by known information or predic-
tion. When input is prepared, chemical compounds present in the database are
docked into the defined binding site of the selected target receptor. There are two
purposes of docking studies. One is to predict accurate ligand binding orientation
referred as “molecular modeling” and the other is to predict activity or binding
affinity referred as “scoring.” A docking result is evaluated by ligand binding orien-
tation through visual inspection and by binding affinity using the scoring function.
Scoring function is designed to predict the biological activity or binding affinity
through the evaluation of interactions between ligands and receptor (Halperin et al.
2002
). Among various docking programs (Table
12.1
), the most widely used pro-
grams are AutoDock (Morris et al.
1998
; Huey et al.
2007
), DOCK (Ewing et al.
2001
), FlexX (Kramer et al.
1999
; Stahl
2000
), Gold (Jones et al.
1995
) , Glide
(Zhou et al.
2001
), Internal Coordinate Mechanics (ICM) (Abagyan and Totrov
1994
) , and Sur fl ex-Dock (Jain
2003
; Kellenberger et al.
2004
) . AutoDock is an
automated flexible docking program designed to predict how small molecules
(ligands) bind into the receptor structure. AutoDock is performed with an empirical
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