The program DOCK calculates possible binding orientations, given the structures of ligand and receptor molecules. The structure of a physiologically important target molecule can be used to find other molecules that may bind it and modulate (usually inhibit) its function. Generally, one searches a large database of commercially available compounds with DOCK, treating each as a possible "ligand," against the structure of a target protein, treated as the "receptor." Simple scoring methods are used to identify the most favorable binding modes of a given molecule, and then to rank the molecules according to these best orientations. The output consists of a large number of candidate ligands in the binding orientations considered most favorable by DOCK. It is then up to human users to look through the molecules and decide which ones are worth pursuing in the real world. It is beyond the scope of this manual to describe DOCK in further detail; please consult the DOCK web page and other information from the program's creators (Kuntz and coworkers).
ViewDock facilitates the selection of compounds by a human user from the output of DOCK (versions 3, 4 and the Northwestern University variant, "NUDock"). In this tutorial, the results of docking a small database of 30 compounds to the protein H-ras (from Protein Data Bank entry 121P) are used to illustrate the workings of ViewDock. See the ViewDock manual page for a more formal description of the program. HearDock works in the same way, but has the additional ability to associate sounds with properties of the docked molecules. To follow along with the tutorial, you first need to download the files ras.pdb (the structure of the receptor, H-ras), gto.pdb (the ligand GTO bound to H-ras in the original PDB file, for comparison with docked molecules), ras.mol2 (the docked molecules output by DOCK 4, in Mol2 format), and setup.com (a file containing commands that set up the viewing context) into your working directory.
On Windows/Mac, click the chimera icon; on UNIX, start Chimera from the system prompt:
unix: chimera
A basic Chimera window should appear after a few seconds. If you like, resize it by placing the cursor on any corner and dragging with the left mouse button. Commands are entered into the Command Line and scaling and clipping operations can be performed with the Side View. One of several ways to start these tools is with Tools... Keyboard... Command Line and Tools... Viewing Parameters... Side View in the menu. Tools can be moved to a convenient location on the screen by dragging with the left or middle mouse button when the cursor is placed on the top bar.
First, open the (previously downloaded) structures of the receptor and its co-crystallized ligand. Choose File... Open. In the resulting dialog, check the option to Keep dialog up after Open. Make sure that the File type is set to PDB, then locate the files. Choose ras.pdb and click Open; after that structure appears, open gto.pdb in the same way. Click Close to dismiss the dialog.
There are several ways to start ViewDock; choose Tools... Docking... ViewDock from the menu. This brings up a dialog requesting the file of molecule orientations previously created by DOCK. Choose and open ras.mol2 (designate the file type as Dock 4 Results). The ViewDock ListBox will appear, along with a thicket of molecules in the graphics window. Move the ListBox aside if it is obstructing the graphics window or any of the other tools.
Now the receptor is in model 0, GTO is in model 1, and the docked molecules are in model 2 (the lowest available model is used for each successive structure opened, and the file of docked molecules was opened last). Individual docked molecules are submodels of model 2 and are specified #2.1, #2.2, and so on.
In most cases, a user is focusing on a particular target protein and will be viewing many different files of docked molecules; thus, many ViewDock sessions will be initiated with the same protein. It can be tedious to repeatedly perform the same operations to display the binding site as desired. One approach is to save a session with the target protein colored and displayed as desired, and then repeatedly restart that session before opening different files of docked ligands with ViewDock. Another approach is to put the necessary commands in a file and simply execute the file as needed. Any files opened by the command file must be in the working directory, or their full pathnames supplied.
The command file (setup.com) used in this tutorial contains:
color aquamarine #0These commands color the receptor (model #0) aquamarine, simplify it to an alpha-carbon trace, and then display all atoms for only the residues within 5 angstroms of a docked molecule. Oxygen atoms in the receptor are colored orange, nitrogens medium blue. The ligand GTO (#1) is shown in magenta ball-and-stick and the docked molecules (#2) are colored by atom type.
chain #0@ca
disp #0 & #2 z<5
color orange #0@o=
color medium blue #0@n=
repr bs #1
color magenta #1
color byatom #2
Opening a command file executes its contents. If setup.com is in the working directory, enter the following in the Command Line (indicated here by Command:):
Command: open setup.comIf setup.com is not in the working directory, use File... Open, set the file type to Chimera commands, and browse to the file and open it. It may take a few seconds to execute the commands.
Show the docked molecules as sticks to make them more prominent:
Command: repr stick #2Throughout the tutorial, adjust the view as desired with the mouse and Side View. Note that one molecule is off in "outer space," while all the rest are clumped together in the binding site. Apparently the rogue molecule could not be docked and remains in the position input to DOCK. It is not near the protein, so it probably has the worst score. This can be checked using the ListBox; if the ListBox has become obscured by other windows, it can be resurrected with Tools... ViewDock... Raise. Click on the lowest line in the top panel of the ListBox (scrolling down if necessary) to choose the worst-scoring molecule. Sure enough, the clump of molecules is undisplayed but the rogue remains, and the lower panel of the ListBox shows that its scores are zero.
There are three mutually exclusive states that can be assigned to docked compounds. Viable compounds are interesting (or have not been looked at yet), Deleted compounds are less interesting but may deserve another look, and Purged compounds are definitely not interesting. Deleted but not purged molecules are included when File... Rewrite is used. Change the status of the rogue molecule to purged by clicking the checkbox under Change Compound State. Note that its listing disappears; make the listing reappear by checking the box next to Compounds... List Purged. Scroll down to the last molecule in the top panel and see that the status of the last molecule is P (purged) while the rest remain V (viable).
Since in this case Name is not very informative, it may be helpful to add other descriptors to the listing in the top panel of the ListBox. Use the Column menu to show Description and Energy score, and to hide Name. The listing can be sorted by any descriptor, whether or not it is shown in the top panel; try Sort... Description (or various other descriptors), but then go back to Sort... Energy score.
Click on the line for the molecule with the best (most negative) energy score to display it and its information. Try clicking various different lines in the ListBox to choose different docked molecules. Chosen lines are highlighted and only the chosen compounds are displayed. Multiple compounds may be chosen at once. Ctrl-click adds to an existing choice rather than replacing it. To choose a block of compounds without having to hold down the mouse button, click on the first (or last) and then Shift-click on the last (or first) in the desired block. Compounds can also be chosen by their descriptor values. The status of all chosen compounds can be changed collectively.
Normally, a user will click on successive lines, examine the compounds in the binding site, and change the status of less interesting compounds to deleted or purged. Additional ways of changing compound status are using picking to prune the set (Selection... Prune) and filtering by the number or presence of hydrogen bonds to the receptor (Chimera... Hydrogen Bonds). See the ViewDock manual page for more details on these features. File... Rewrite is then used to write a file containing just the viable and deleted compounds, which can be input to a later ViewDock session. Often several sessions are needed to whittle the list down to sufficiently few compounds.
Instead, for tutorial purposes, change the display and then play a "movie" which flips through the compounds in the site. Undisplay GTO and place a solid surface on the binding site (receptor residues within 7 angstroms of GTO; this may take a minute):
Command: ~disp :gto
Command: surf #0 & :gto z<7
Movie... Play starts the movie, which "pages through" all compounds listed in the top panel of the ListBox in the order that they are listed, regardless of status. The movie will loop continuously through the list until halted with Movie... Stop. It is possible to move the molecules around and change the view during the movie. The length of time each compound is shown can be controlled with Movie... Options. If molecules are "unlisted" using the checkboxes in the Compounds menu, they are not included in the movie; in addition, the order of display depends on how the molecules are sorted. No matter how the molecules are sorted in the ListBox, however, they remain in the original order (minus any purged compounds) in output files created with File... Rewrite. Once you have seen enough, stop the movie and exit from Chimera.