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User Guide

Here is the step-by-step guide for using the Ligand Explorer application. If you are
running the applet from the PDB site, please start from step 4:

1. Once you have successfully installed the Ligand Explorer application on your
computer, you should see a"Ligand Explorer" icon on your desktop. Click on this
icon to start the program.

2. If you know the pdb id of the structure file you want to examine, you can load the
structure by

(a) type in the pdb id in the text box and then return(press the enter key on your
keyboard);

or
(b) click on the right side of the text box(see the screenshot below), wait for the pdb
list to show up and then select your pdb id.

3. You can also load a pdb/mmCIF structure file by going to File/Open.

http://users.sdsc.edu/~qzhang/ligand/help/userGuide.htm 4/23/2004

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4. When the structure is loaded, the program dynamically generates the ligand list
associated with this structure and displays it on the left panel. In the structure viewer,
the protein backbones are shown in tracelines (the same color scheme as in the
sequence viewer on the top), and all the ligands are shown in ball and stick.

Hold down the left button of the mouse and then drag to rotate the structure, hold down
the middle button and then drag to zoom in and out, and hold down the right button of
the mouse and then drag to move up/down and left/right. Click on the "Reset" button on
the left panel to bring the structure to the initial position.

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Click on a protein residue in the sequence viewer, the full residue will be draw in the
structure viewer and the chain id and residue id of this residue can be found in the
status bar:

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Click on a protein fragement in the structure viewer, this fragment will be highlighted in
the structure viewer and the sequence viewer. Information about this fragment will be
given in the status bar:

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5. Select a ligand of interest and click on "Apply", the program will center the view
around this ligand.

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You can click on an atom to see the atom name in the status bar; or click on a bond to
see the names of the atoms that form this bond.

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6. If you choose to examine the hydrophilic (H-bond) interactions for ATP_1 ligand,
select this option and click on "Apply". In the sequence viewer (1 in the screenshot
below), the protein residues that interact with this ligand within your specified range will
be highlighted in red (2). Mouse over to any protein residue in the sequence viewer, you
will see the three-letter code and its residue id (3). In the structure viewer, the
interacting protein residues will be fully drawn (4), and the name of each interacting
protein residue is displayed at its alpha-C position in the format of
"chain_id:three_letter_code residue_id" (5).

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You will see a summary of calculated interactions in the status bar:

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To examine the details of the binding site, you can use the options in the Analysis
menu: "Measure Distance" measures the distance between any two atoms in the
display, "Measure Angle" measures the angle between any three atoms, and "Dihedral
Angle" measures the torsion angle of four contiguous atoms. For example, if you want
to check the angle of the three atoms highlighted in the screenshot below, select
"Measure Angle".

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You will see a dialog. Enter the name of the atom by clicking on this atom in the
structure viewer or typing its name into the text box, then click on "Execute".

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The caculated angle will be shown in the status bar.

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7. Click on the interacting protein residue (1 in the screenshot below) in the sequence
viewer, it will highlight the protein residue in the structure viewer (2). Note if the feature
is still under construction, then a message will tell so in the status bar (3); if an error
occured while you are running the program, the status bar is where you look for the
error message.

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8. You can also turn the distance label off. The screenshot below shows the
hydrophobic interactions with distance label off.

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9. You can adjust the interaction threshold. The following shows hydrophobic
interactions between 1.9Å to 5.0Å.

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10. You can examine different interactions at the same time. For example, the following
shows the hydrophobic interactions (magenta dashed lines, 1 in the screenshot below)
and hydrophilic interactions(green dashed lines, 2).

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11. Select "Other" to see other ligand-protein interactions.

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12. Select "ligand-H2O-protein" to see ligand-H2O interactions and ligand-protein
interactions bridged by ordered H2O molecules.

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13. Select "inter-ligand" to see inter-ligand interactions.

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14. If you would like to see the details of an atom or a particular bond, go to Tools in the
menu and click on "Show Inspector".

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You will see a poped-up table.

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Click on an atom in the structure viewer, the program will populate the table with
detailed information about this atom.

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Click on a bond in the structure viewer, the program will populate the table with detailed
information about this bond.

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15. If you would like to save the image in the structure viewer, select "Save Image" in
File menu.

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You will see a popped-up window. Select a format (.jpg or .png) and fill in the "File
Name"(Note you need to include .jpg or .png in your file name). Click on Save.

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Your saved image looks like this:

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16. You can save interactions into three different file format: .xls(Microsoft Excel), .txt,
or .doc. To save interactions, click on "Save Interactions" in "File" menu.

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You'll see a dialog. Select directory and type in the file name(Don't forget to indicate the
file format by typing in the file extension---.xls, .txt, or .doc).

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This is your saved interaction file in excel format:

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