The program DOCK postulates binding orientations, given structures of the "ligand" and "receptor" molecules. It is often of interest to use the structure of a molecule that is important in physiology or disease to find other molecules to 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 (as opposed to the virtual) 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 Kuntz and coworkers, who have created and developed the method over the last several years.
ViewDock facilitates the selection of compounds by a human user from the output of DOCK version 4. In this tutorial, the results of docking a small database of 30 compounds to the protein H-ras (from Protein DataBank entry 121P) are used to illustrate the workings of ViewDock. See the ViewDock manual page for a more formal description of the program. Note that 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 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 (a file containing commands to set up the viewing context) into your working directory.
On UNIX, start Chimera from the system prompt:
unix: chimeraOn Windows, click the chimera icon.
A basic Chimera window should appear after a few seconds. Commands are entered into the Command Line and scaling and clipping operations can be performed with the Side View. There are several ways to start each of these tools; choose Tools... Keyboard... Command Line and Tools... Viewing Parameters... Side View from the menu. Move each tool to a convenient location on the screen by dragging with the left or middle mouse button when the cursor is placed on the bar across the top of the tool. If you like, resize the main Chimera window by placing the cursor on any corner and dragging with the left mouse button.
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 the previously downloaded file ras.mol2. The ViewDock ListBox and a thicket of white molecules in the main graphics window should appear. Move the ListBox aside if it is obstructing the graphics window or any of the other tools.
In most cases, the 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. Since it is tedious to repeatedly enter the same set of commands to display the binding site as desired, it can be helpful to put this set of commands in a file and then just source the file in the Midas Emulator. The contents of the source file depend on personal preference and are determined by trial and error. Of course, one may prefer to type the commands in each time rather than using a source file.
The contents of the source file used in this tutorial, setup, are shown below:
color byatomThese commands color the docked molecules according to atom type, open the receptor structure and simplify it by showing only side chains within 5 angstroms of any docked molecule, open the co-crystallized ligand GTO, show it as magenta ball-and-stick, and color heteroatoms in the receptor orange (oxygens) and medium blue (nitrogens). Enter the following in the Command Line (indicated here by Command:):
open ras.pdb
color aquamarine #1
chain @ca
disp #1 & #0 z<5
open gto.pdb
repr bs :gto
color magenta #2
color orange #1@o=
color medium blue #1@n=
Command: source setupNow the docked molecules are in model 0, the receptor is in model 1, and GTO is in model 2 (the lowest available model is used for each successive structure opened, and the file of docked molecules was opened first). Individual docked molecules are submodels of model 0 and are specified #0.1, #0.2, and so on.
To get a better perspective on the locations of the docked molecules and make them more prominent:
Command: window #0Note that one docked 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. 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. Now that the clump of docked molecules have been undisplayed, the magenta co-crystallized ligand GTO is more visible.
Command: repr stick #0
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 with the checkbox near the bottom of the ListBox. Note that its listing disappears; make the listing reappear by checking the box next to ListBox... List purged compounds. 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).
Use the Side View and mouse manipulation in the graphics window to get a better view of the binding site; continue to use these throughout the tutorial as desired.
Since in this case Name is not very informative, it may be helpful to add molecule Description to the listing in the top panel of the ListBox. Try Column... Add... Description and Column... Delete... Name. This 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 best-scoring molecule in the ListBox (scroll up to the top of the top panel, if necessary) to display it and its information. Try clicking on different lines in the ListBox to show different docked molecules. Note that it is possible to choose several lines at once and display all of the corresponding compounds; clicking a Compound State checkbox (near the bottom of the ListBox) will then change the status of all of the chosen compounds.
Normally, the user will click on successive lines in the ListBox, examine each compound 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 #1 & :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. Note that 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 ListBox menu, they are not included in the movie; in addition, the order of display depends on how the molecules are sorted (controlled with the Sort menu). 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.