Tool: ViewDock

ViewDock 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. See also: an example file of compounds docked to H-ras (the protein part of PDB entry 121p), H-Bonds, Clashes/Contacts, Dock Prep

Possible formats of docking results:

• Mol2 (.mol2) from
  • UCSF DOCK v4-6
  • UCSF DOCK v3.7 (however, the ligand descriptors in condensed tabular form will not be shown)
  • GOLD
  • MOE
• AutoDock Vina PDBQT (.pdbqt) (Protein Data Bank with partial charge Q and atom type T format)
• Glide Maestro (.mae, .maegz) – to be recognized as docking results, the file must contain the r_i_docking_score descriptor; other Maestro files (those not produced by Glide) may not contain this descriptor
• SwissDock modified PDB format (open with format swissdock; the ligand and receptor files can be opened in either order, and with two commands or a single command)

By default (open command with showTool true), opening a file that contains multiple docked ligands or ligand poses will automatically start the ViewDock interface. Alternatively, one or more such files can be opened with showTool false, and subsequently the ViewDock tool can be started from the Binding Analysis section of the Tools menu

The docking results and scores (if any) are listed in a table that can be manipulated like other panels in ChimeraX (more...).

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ViewDock Table

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 structures and their data are saved in sessions.

One or more rows can be chosen (highlighted) in the list by clicking and dragging with the left mouse button; Ctrl-click (or command-click if using a Mac) toggles whether a row is chosen. Choosing rows displays the corresponding compounds and hides the others. Choosing a single compound (row) displays all of its descriptor values in the lower part of the panel and allows setting its Compound Rating as good, maybe, or bad or (unrated). If multiple compounds are chosen, their descriptors are not shown, but their ratings can be changed collectively. The ratings can also be adjusted with hotkeys. Below each rating button is a hide checkbox, which if activated will hide all of the corresponding compounds in both the ViewDock table and the graphics window. The hidden models will still be listed in the Model Panel.

When the ViewDock 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 chooses the next (previous) compound in the list. The list can also be navigated with the next docked mouse mode .

The first two columns in the table are generated automatically:

• ID – model number
• Rating – whether unrated or assigned as good, maybe, or bad by the user

Any additional columns that appear when ViewDock is first started reflect information read from the input file(s). Clicking a column header sorts by the values in that column, and dragging it left or right allows reordering the columns. Checkboxes under the list of compounds specify which columns of information to include in the table of hits, with buttons:

• All – show all columns
• Default – restore the previously saved preference for which columns are shown
• Standard – use “factory default” set of initially displayed columns
• Set Default – save the currently shown set as a user preference
• Toggle Controls – show/hide the checkbox section

Buttons above the table:

• HBonds – calculate and add a column for the number of H-bonds between each compound and all other atoms (excluding the other docked compounds) using the H-Bonds tool
• Clashes – calculate and add a column for the number of clashes between each compound and all other atoms (excluding the other docked compounds) using the Clashes tool

  For the purposes of identifying H-bonds and clashes, ligand residues in the receptor model not meant to be considered should be deleted beforehand. In addition, any models other than the receptor and its docked compounds should be spatially separated from them or closed.

• Save... save all compound structures listed in the table and their descriptors (including ratings) to a Mol2 file; the file can be reopened later for further analysis with ViewDock
• Close – close the currently chosen compounds and remove their rows from the table

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ViewDock Hotkeys

Compound-rating hotkeys can be activated by checking Hotkeys active in the ViewDock dialog's context menu. With hotkeys enabled and mouse focus in the ViewDock dialog or the 3D graphics window:

• typing g/m/b/u will rate the currently chosen compounds as good/maybe/bad/(unrated)
• down (up) arrow keys navigate the table by choosing the next (previous) compound, unless mouse focus is in the 3D graphics window and there is a selection, in which case they navigate the selection hierarchy
• Esc turns off the ViewDock hotkeys; they can also be disabled (or re-enabled) using the ViewDock context menu

ViewDock hotkey status is remembered across ChimeraX sessions in the user preferences.