ViewDockX is a tool for the interactive analysis of molecular docking results. Users can click through a list of docked compounds (or different poses of the same compound) to view them individually in the context of a binding site. Results can be sorted, rated, and saved, and scores or other numerical descriptors can be plotted. See also: hbonds, clashes, an example file of compounds docked to H-ras (the protein part of PDB entry 121p)
After one or more files of docking results have been opened, a table listing the different compounds or poses can be shown by starting ViewDockX from the Tools menu or by using the command:
– or –
...the latter to limit the table to only a subset of the docked compound models currently open. The table and associated plots can be manipulated like other panels in ChimeraX (more...).
In the table of docking results, the rows are different compounds or different positions of a compound, and the columns show additional data read from the input, typically including compound names and docking scores.
The checkboxes in the first column control which docked compounds are shown. Clicking anywhere on a row checks the corresponding box and unchecks the others. Clicking directly on the boxes allows showing multiple compounds at the same time.
The second and third columns are generated automatically:
Any additional columns that appear when ViewDockX is first started reflect information read from the input file(s).
A text-search box allows finding hits that contain terms of interest. A pull-down menu to the right of the search box can be used to adjust which of the available columns of information are shown in the table. Clicking a column header sorts by the values in that column.
When the ViewDockX dialog has the mouse focus and a single compound is shown (it may be necessary to click on the row for that compound after interacting with other windows), pressing the keyboard down (up) arrow key hides the compound and shows the next (previous) compound in the list. The next docked mouse mode or commands viewdockx down and viewdockx up can be used to do the same thing. If multiple compounds are shown, the entire set of shown compounds shifts one position in the list for each use of the down (up) arrow key or equivalent command.
Buttons above the table:
Because all other atoms besides the docked compounds are treated as the receptor for identifying H-bonds and clashes, any atoms not meant to be considered (generally solvent, co-crystallized ligands, etc.) should be deleted beforehand. In addition, any models other than the receptor and its docked compounds should be spatially separated from them or closed.
ViewDockX table status is saved in sessions, including which rows are checked, but not its window size or location.
Multiple graph/plot windows can be shown for the same set of docking results.
Clicking the Graph button near the top left of the ViewDockX table allows plotting all compounds along the X-axis versus one or more numerical descriptors on the Y-axis. One of the numerical descriptors can be chosen for the Sort order, and all or a subset of them as values to Graph. The data can also be shown as a histogram with specified number of bins.
Clicking the Plot button near the top left of the ViewDockX table opens another window for plotting numerical descriptors versus each other. Up to two plots can be shown in the same window, with numerical descriptors chosen for the X and Y axes of each.
A “halo” around a plotted point indicates that the compound is currently shown in the graphics window. Pausing the cursor over a plotted point shows the compound's descriptor values. Clicking a plotted point or histogram bar shows the corresponding compound(s) in the graphics window and hides the others.