# DOC, DOCK

NAME
DOC, DOCK - prepare two structures for docking.
SYNOPSIS
DOC identifier_1 identifier_2
DOC OFF
DOCK identifier_1 identifier_2
DOCK OFF
DESCRIPTION
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.
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.
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.
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.
KEYWORDS
The keyword OFF is the only keyword which may be used with the command DOCK. DOCK OFF is used to hide docking window.

KEYWORD | DESCRIPTION
OFF | Hide docking window.

PARAMETERS
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.

PARAMETER | DESCRIPTION
identifier_1 | Identifier of the first molecule. (substrate, for example).
identifier_2 | Identifier of the second molecule. (inhibitor, for example).

EXAMPLE
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 ( PDB code 1STF).

STEP1:
Load the first structure:
load file1.pdb
Change the color. Cyan-blue might be
a good choice:
color cyan-blue

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

STEP 3: Push the first structure to the corner. Load the second structure: load file2.pdb Change color. Red is recommended here: color red | STEP 4: Make the plane visible and divide the second structure in two parts. Change drawing style for atoms or bonds. plane move plane (... now rotate and translate the plane) sel above atom sp2 Reset movement controls: move all
STEP 5: Execute DOCK command: dock 1 2 | Rotate the second (top) structure. Check the relative arrangement of hydrogen bond donors and acceptors. The projections of these side chains are given in docking window.

NOTES
(1) If two structures are close, some important atoms might be unvisible (hidden by some closer atoms). Use slab to cut slices through structure(s).
(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.
RELATED COMMANDS
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.
REFERENCES
(1) Kamphuis, I. G., Kalk, K. H., Swarte, M. B. A. and Drenth, J. (1984). J. Mol. Biol. 179, p. 233.
(2) Stubbs, M. T., Laber, B., Bode, W., Huber, R., Jerala, R., Lenarcic, B. and Turk, V. (1990). EMBO J. 9, p. 1939.