MMPF, pose filtering, macromolecular
Macromolecular Pose Filtering Panel
Filter ensembles of macromolecular complexes based on structure properties, residue properties, or HDX score criteria.
To open this panel, click the Tasks button and browse to Biologics → Macromolecular Pose Filter.
- Using
- Features
- Additional Resources
Using the Macromolecular Pose Filtering Panel
The panel reads ensembles of structures of complexes generated through docking with PIPER or molecular dynamics with Desmond. It can also use orthogonal data such as Hydrogen Deuterium Exchange (HDX) results, generic CSV files, or lists of interface residues that can then be used to set criteria for selecting poses that meet user specific constraints.
For more information regarding the scoring function used for pose filtering based on HDX data, see this publication.
Macromolecular Pose Filtering Features
- Choose task menu
- Pose filtering
- View filtering results
- Job toolbar
- Status bar
- Choose task menu
- Select the task to be used: Pose filtering, or to View filtering results. The configurations of the panel and the corresponding options available are dependent on the task selection, as shown in the images above.
- Pose filtering configuration
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Use this configuration to choose complexes to filter or to visualize structures. In Pose filtering configuration, the following options become available:
- Use poses from option menu
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Choose entries with multiple protein-protein poses (all of which must be conformers of the same set of interacting proteins) from:
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Project Table (selected entries) —choose this option and click the Load button to use poses from the Project Table.
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File —choose this option and click the Browse button to select an input file.
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- PP Interface section
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Select the chains that define each protein partner in the protein-protein interface. Both chain sets must be specified when using HDX Score filtering or the More options calculations.
- Filter poses by options
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Filter the poses by selecting an option:
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Structure properties —Click the Import properties link to browse for a CSV file containing the properties of interest to add to the existing structure properties. Alternatively, you can use the existing properties without adding an additional CSV file. A message appears at the bottom of the panel with the number of properties that are successfully imported.
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At the bottom of the panel, the Property filters table displays the specified filters.
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The Add Filter option menu allows you to specify additional properties to filter by, and allows for filters to be combined with boolean operators to refine the results.
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Residues properties —Click to view the Property filters table, which displays filters based on the constraints specified, such as "Interfaces with" and "Solvent Accessible Surface Area," and the associated options.
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As with Structure properties, the Add Filter option menu allows you to specify additional properties to filter by, and allows for filters to be combined with boolean operators to refine the results.
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Click the Define link to define a Residue set in a separate dialog box. Click the + icon to define additional chains.
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The Min # of residues that must match the filter text box is set by entering a numerical value and by using the arrow buttons to adjust the value.
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When selected, the Color by residue property option enables further options to set gradient colors to specified properties:
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Property —select a property to color-code. The %D property is the default.
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Color Gradient —The minimum and maximum values of the column are selected as the start and stop values for the gradient, and these values can be edited in the corresponding text boxes. Colors are selected by clicking the colored square icon and selecting a color from the menu.
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Click the + icon to add another level of gradient with the second value as the median of the range. Click the - icon to remove an added range.
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HDX Score —Click to view the Calculate HDX score table, which displays the input parameters for HDX scoring.
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Choose the number of binding partners for which HDX data is available from the No. of proteins with HDX data option menu.
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Each binding partner section provides options for loading an HDX data file and selecting the Bound protein state and Unbound protein state. When No. of proteins with HDX data is set to 1, only Binding Partner 1 shows these options. Binding Partner 2 instead displays the protein chain names from the Chain set 2 selection.
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Click the Browse button next to HDX data file: to select a data file. Note: The format of this file needs to meet the standard specific in this publication.
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The Protein chain name text shows the chains selected in Chain set 2 for Binding Partner 2. Only present when No. of proteins with HDX data is set to 1.
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The Delta %D cut-off text box allows for a numerical value to be entered, where only residues with the percent change in deuteration above the cutoff value chosen will be included in the scoring.
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- More options link
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Click this link to display additional calculation options. These options are available for all filter types. Chain set 1 and Chain set 2 must be specified when either option is selected.
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Calculate prime energies in place —Select this option to calculate Prime energies for each pose.
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Calculate each residue's frequency of occurrence at the protein-protein interface —Select this option to calculate a binary interaction matrix that indicates whether each residue in the first protein interacts with each residue in the second protein.
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- View filtering results
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Use this configuration to view filtering results and to make the following options available:
- Load results from option menu
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Click the Browse button to select the results directory to load from. The returned poses are ranked based on the criteria specified.
- Filter details link
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Clicking this link enables the following options:
The Residue filters table displays a list of poses based on the defined filtering criteria.
Click the Modify Query link to rerun the query using a different set of parameters.
Click the Filter details link again to collapse the table and display the Filter results table.
- Filter results table
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If filtering using structure or residue properties, the table displays a list of poses which satisfy the filtering criteria.
If filtering using HDX, the table displays a plot of Ligand HDX Score on the y-axis and Receptor HDX Score on the x-axis. Each point on the plot can be linked to the Hierarchy Table in the Workspace. If a Ligand Scores data column is not provided, the table is hidden.
Hovering the cursor over a scatter point on the table displays a tooltip with the structure title, receptor score, and ligand score.
- Save results menu
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Click the menu and select an option to save the results: Save Image, or Export as CSV.
- Workspace display link
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This link is available if a 3D structure and a data file associated with residues in that structure are loaded. Click the link to open the Workspace display menu, containing settings to color-code structures based on user specifications.
- When selected, the Color by residue property
- Property —select a property to color-code. The %D property is the default.
- Color Gradient —The minimum and maximum values of the column are selected as the start and stop values for the gradient, and these values can be edited in the corresponding text boxes. Colors are selected by clicking the colored square icon and selecting a color from the menu.
- Click the + icon to add another level of gradient with the second value as the median of the range. Click the - icon to remove an added range.
- When selected, the Color by residue property
- Add to Project Table button
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When this button is activated, the selected points (poses) on the plot are added to the Project Table, and a new group is created from the selection.
Job toolbar
Manage job submission and settings. See Job Toolbar for a description of this toolbar.
Status bar
The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.
Use the Reset button 
to reset the panel to its default settings and clear any data from the panel.
The status bar also contains the Help button 
, which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a 
button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.