MM-GBSA Residue Scanning/Humanize Antibody Viewer Panel

MM-GBSA Results Viewer Panel Features

• Load results from option menu
• Import to Project Table button
• Load button
• File name text box and Browse button
• Mutations table
• Workspace Display link
• Graph representation section
  • Graph property option menu
  • X-axis and Y-axis menus
  • Plot area
  • Sync selection with mutations table option
• Create LOGO Plot link
• Send to FEP button menu
• Export button menu
• Reset button

Load results from option menu

Choose the structure source for the mutation results.

• Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries. When this option is selected, a Load button is displayed to the right.
• File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.

Import to Project Table button

Add the selected entry or entries for the structure source to the Project Table and to the Workspace. When one or more entries is selected in the Mutations table (indicated by a yellow highlight), clicking the Import to Project Table button will selectively import those mutations. This button is enabled if any of the selected rows in the Mutations table are not imported.

Load button

Load the results from the selected Maestro entries into the results table. This button is only displayed when you choose Project Table as the source for the results.

File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.

Mutations table

This table lists the residues that were mutated, with the identity of the original residue and of the mutated residue for each mutation that was performed. It also shows the change in the following properties for each residue:

• SASA (total, polar, and nonpolar)
• pKa
• Affinity
• Hydropathy
• Total rotatable bonds
• Stability (in solution and in gas phase)
• Surface complementarity

The table can be sorted by clicking on the column headings.

Any rows in the table whose structure has been imported will be marked with an eye icon, and the structure will be included in the Workspace in accordance with the selected Workspace display options.

When you select rows in the table, the Workspace view zooms in to the corresponding residues if you have Fit to selected on. The mutations in the selected rows can be sent as input to the FEP Protein Mutation Panel, either by right-clicking in the selection and choosing Send Selected to FEP+ or by using the Send to FEP button menu. The mutations must be single mutations from the original protein.

Workspace Display link

Set options for display of mutations in the Workspace. Opens a menu to make the settings.

• Display original structure in gray—Display the original structure in gray in the Workspace as well as the mutated structure. This allows you to compare mutations with their originals.
• Fit to selected—Fit the Workspace view to the selected residues (table rows).

Graph representation section

Choose the property to graph in the plot area below. The properties are those displayed in the Mutations table.

Property option menu

Choose the property to graph in the plot area below. The properties are those displayed in the Mutations table.

X-axis and Y-axis menus

Use the dropdown menus to change settings for the axes. For results with both stability and affinity, the x-axis shows stability and the y-axis shows affinity. For results with stability, the x-axis menu is replaced with the row number, while the y-axis shows the affinity.

Plot area

This area displays a plot of the property chosen from the Property option menu as a function of the row number in the table (residue position). Dragging out a box on the plot highlights the rows in the table that correspond to the points inside the box. A tooltip appears when a data point in the chart is hovered over, and displays the properties for both the x and y axis along with the values.

Sync selection with mutations table option

When you drag out a box over points in the plot, the corresponding rows of the table are selected, and the residues are selected in the Workspace. Selecting table rows highlights the corresponding rows in the chart with a pink color. This option is enabled by default.

Create Logo Plot link

Display a LOGO plot of the mutation results in a separate panel. The image created for this panel is written to the working directory as jobname.png, and the data used to create the image are written to jobname.csv.

Only available for Affinity Maturation.

Send to FEP button menu

Send the mutations as input to the FEP Protein Mutation Panel. The mutations must be supported for FEP+ calculations, which includes single mutations and multiple simultaneous mutations (multi-site mutations). The menu allows you to send either the mutations selected in the Mutations table (Send Selected) or the entire set of mutations (Send All) to this panel. The panel opens with the protein selected and the mutations set. The calculation type is set as Selectivity if affinity was selected to be calculated as part of the MM-GBSA Residue Scanning Panel or the Antibody Humanization: Residue Mutation Panel, and otherwise set as Stability. You can then make any other settings and submit the job.

Export button menu

Export data or images to a file. A file selector opens, in which you can navigate to a location, select the file type, and name the file.

• Mutations—export the mutations to a file. You can export the data from the table to a CSV file, the original and mutated structures to a Maestro file, or the list of mutations to a text file, one per line. Each mutation in is in the format chain:number->resname.

• Graph Image—export the current graph as an image. You can choose from a range of image formats.

• Export Selected Only option—export the selected mutations only; by default all mutations are exported.

Reset button

Delete all data from the panel.