/usr/share/doc/garlic-doc/commands/doc.html

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<title>
DOC, DOCK
</title>
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DOC, DOCK

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<font color=#880000>
<b>
NAME
<br>
</b>
</font>


DOC, DOCK - prepare two structures for docking.
<br><br>


<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
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DOC identifier_1 identifier_2
<br>
DOC OFF
<br>
DOCK identifier_1 identifier_2
<br>
DOCK OFF
<br><br>


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<b>
DESCRIPTION
<br>
</b>
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The command DOCK prepares two structures for docking. Before executing this
command, two molecules (structures) have to be loaded. For each structure a
region on the surface should be selected as a candidate region for interaction
with another molecule. For example, if the first molecule is the substrate,
the active site has to be identified as the region where the inhibitor should
be placed. Assuming that another molecule is the inhibitor, the side which is
expected to interact with the substrate should be identified.
<br><br>

When both molecules are ready for docking, the command DOCK should be
executed. The identifiers of both molecules have to be issued as arguments.
Both molecules will be translated and rotated to position and orientation
suitable for docking. The first molecule will be moved to the bottom of the
main window, with the selected region visible on the upper side. The second
molecule will be placed atop the first molecule, with the selected region
facing the first molecule.
<br><br>

Further, a special docking window will be opened, showing the orthogonal
projections of polar side chains as symbols. The polar side chains of both
molecules are projected to the plane associated with the first molecule.
Cyan symbols belong to the bottom molecule (the first one) and red symbols
belong to the top molecule. Hydrogen bond donors are shown as crosses,
acceptors as circles, and side chains which are both hydrogen bond donors
and acceptors are shown as crosses in circles.
<br><br>

The user might be able to combine two structures, using the information
visible in both the main garlic window and in docking window. However, this
routine is still quite naive, so don't expect too much. Docking is not an
easy game. I hope that this command will be useful at least for educational
purpose.
<br><br>


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<b>
KEYWORDS
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</b>
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The keyword OFF is the only keyword which may be used with the command DOCK.
DOCK OFF is used to hide docking window.
<br><br>


<table border=2 cellspacing=2 cellpading=0>

<td align="left">

KEYWORD

</td>

<td align="left">

DESCRIPTION

</td>

<tr>

<td align="left">

OFF

</td>

<td align="left">

Hide docking window.

</td>

</table>

<br>

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<b>
PARAMETERS
<br>
</b>
</font>


Except when used in combination with the keyword OFF, the command DOCK should
be followed by two structure identifiers. If you have forgotten these
numbers, just move the mouse pointer over the structure(s) and find the
identifier(s) in the output window (the bottom right corner). The order is
important: the first molecule will be placed to the bottom of the main window,
while the second will be placed atop the first one.
<br><br>


<table border=2 cellspacing=2 cellpading=0>

<td align="left">

PARAMETER

</td>

<td align="left">

DESCRIPTION

</td>

<tr>

<td align="left">

identifier_1

</td>

<td align="left">

Identifier of the first molecule.
<br>
(substrate, for example).

</td>

<tr>

<td align="left">

identifier_2

</td>

<td align="left">

Identifier of the second molecule.
<br>
(inhibitor, for example).

</td>

</table>

<br>

<font color=#880000>
<b>
EXAMPLE
<br>
</b>
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The example below shows how to prepare two structures for docking. In this
example, the first structure is papain (reference 1) and the second
structure is stefin (reference 2). The structure of the complex is known
(
<a href="http://www.rcsb.org/pdb">
PDB
</a>
code 1STF).
<br><br>


<table border=2 cellspacing=2 cellpading=0>

<td align="left">

STEP1:
<br>
Load the first structure:
<br>
<font color=RED>
load file1.pdb
</font>
<br>
Change the color. Cyan-blue might be
<br>
a good choice:
<br>
<font color=RED>
color cyan-blue
</font>

</td>

<td align="left">

STEP 2:
<br>
Make the plane visible:
<br>
<font color=RED>
plane
</font>
<br>
Prepare to move the plane:
<br>
<font color=RED>
move plane
</font>
<br>
Use plane to divide structure in two parts.
<br>
The active site should be above the plane.
<br>
Change drawing style for atoms or bonds.
<br>
Here the spacefill style is used. This is
<br>
bad idea if using slow machine.
<br>
<font color=RED>
sel above
</font>
<br>
atom sp2
<br>
Reset movement controls:
<br>
<font color=RED>
move all
</font>

</td>

<tr>

<td align="left">
<img src="papain1.jpg">
</td>

<td align="left">
<img src="papain2.jpg">
</td>

<tr>

<td align="left">

STEP 3:
<br>
Push the first structure to the corner.
<br>
Load the second structure:
<br>
<font color=RED>
load file2.pdb
</font>
<br>
Change color. Red is recommended here:
<br>
<font color=RED>
color red
</font>

</td>

<td align="left">

STEP 4:
<br>
Make the plane visible and divide the
<br>
second structure in two parts. Change
<br>
drawing style for atoms or bonds.
<br>
<font color=RED>
plane
</font>
<br>
move plane
<br>
(... now rotate and translate the plane)
<br>
<font color=RED>
sel above
</font>
<br>
atom sp2
<br>
Reset movement controls:
<br>
<font color=RED>
move all
</font>

</td>

<tr>

<td align="left">
<img src="stefin1.jpg">
</td>

<td align="left">
<img src="stefin2.jpg">
</td>

<tr>

<td align="left">

STEP 5:
<br>
Execute DOCK command:
<br>
<font color=RED>
dock 1 2
</font>

</td>

<td align="left">

Rotate the second (top) structure. Check
<br>
the relative arrangement of hydrogen bond
<br>
donors and acceptors. The projections of
<br>
these side chains are given in docking
<br>
window.

</td>

<tr>

<td align="left">
<img src="dock1.jpg">
</td>

<td align="left">
<img src="dock2.jpg">
</td>

</table>

<br>

<font color=#880000>
<b>
NOTES
<br>
</b>
</font>


(1) If two structures are close, some important atoms might be invisible
(hidden by some closer atoms). Use slab to cut slices through structure(s).
<br><br>

(2) Don't forget to catch the right structure before applying some
transformation. By default, after the command DOCK is executed, the movement
controls are attached to the second (top) structure.
<br><br>


<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>


LOAD is used to load the specified file (structure, molecule). MOVE is used
to define which object should be moved (structure, plane or both). PLANE is
used to manipulate the plane associated with the structure. CATCH is used to
attach the movement controls to a chosen structure.
<br><br>


<font color=#880000>
<b>
REFERENCES
<br>
</b>
</font>


(1)
Kamphuis, I. G., Kalk, K. H., Swarte, M. B. A. and Drenth, J. (1984).
J. Mol. Biol. 179, p. 233.
<br><br>

(2) Stubbs, M. T., Laber, B., Bode, W., Huber, R., Jerala, R., Lenarcic, B. 
and Turk, V. (1990). EMBO J. 9, p. 1939.
<br><br>


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garlic-doc 1.6-1 / usr / share / doc / garlic-doc / commands / doc.html
