Residue Analysis Panel

Run an analysis of the protein in the Workspace to produce properties of the residues, including hydropathy, energies, solvent-accessible surface areas, and rotatable bonds.

To open this panel, click the Tasks button and browse to Biologics → Residue Analysis.
To open this panel from the entry group for the results of an antibody structure prediction job, use the Workflow Action Menu .

  • Using
  • Features
  • Additional Resources

Using the Residue Analysis Panel

Identifying stable or unstable residues, or residues with desirable or undesirable properties may be a useful precursor to mutation studies. These properties can be used to identify residues with either desirable properties or undesirable properties, which may suggest residues that could be mutated to improve the protein properties.

Before analyzing a protein, you should prepare it with the Protein Preparation Workflow Panel. To analyze the properties of a protein, first display it in the Workspace, and then click Run. If you want to analyze particular residues, select them first before clicking Run. When the job finishes, the residue table is filled in and the first property is plotted below. You can export the table data to a CSV file by clicking Export and then providing the file name in the file selector that opens.

If you want to view properties for water molecules or het groups (ligands, cofactors, ions), select the appropriate Show option below the table.

To highlight one or more residues in the Workspace, select the table rows. If you have Fit on selection selected, the view zooms in (or out) so that these residues occupy most of the Workspace.

To examine a particular property for all residues, you can make a plot of the property as a function of residue position. Choose the property from the Graph property option menu to display the plot. You can use the plot to select residues by moving the dotted lines to enclose the residues you are interested in. For example, you might want to select residues that have significantly larger or significantly smaller values of the properties than the average, by moving the upper or the lower red dotted line to enclose just those data points.

To run a residue analysis from the command line, you can use the following command. Run the command with -h for more information.

$SCHRODINGER/run residue_analysis_backend.py

For information on command options, see residue_analysis_backend.py Command Help.

Residue Analysis Panel Features

Analyze options

Select an option for the residues to analyze, from Entire Workspace structure or Selected Workspace residues. For the latter option, select the residues in the Workspace that you want to analyze.

Residue table

Lists the residues and their properties. Selecting rows in the table highlights the residues in the Workspace, and if Fit on selection is selected, zooms in to those residues. You can sort the table by clicking on the heading of the column you want to sort by. A second click changes the sort direction. The table columns are described below.

Residue Residue identity: chain, residue number and insertion code, 3-letter name.
Hydropathy Hydropathy calculated using the Kyte-Doolittle scale, normalized by the solvent accessible surface area.
Potential Energy Sum of the residue-based internal energy and the non-bonded interaction energy (vdW, electrostatic) between the residue and the remainder of the system.
Internal Energy Sum of energies arising from intra-residue bonded interactions (bonds, angles, torsions) and intra-residue non-bonded interactions (vdW, electrostatic).
Interaction Energy Energy of interaction between this residue and all other atoms.
SASA (Non-polar) Solvent-accessible surface area of nonpolar atoms of this residue
SASA (Polar) Solvent-accessible surface area of polar atoms of this residue
SASA Total solvent-accessible surface area of this residue
Rotatable bonds Number of rotatable bonds in this residue
Fit on selection option

Select this option to zoom in on residues when they are selected in the table.

Show waters option

List water molecules in the table of residues.

Show hets option

List het groups (ligands, cofactors, ions) in the table of residues.

Graph property option menu

Choose a property from this option menu to plot in the property plot area.

Property plot area

This area displays a plot of the property chosen from the Graph property option menu as a function of the row number in the table (residue position). The plot has a toolbar and a display area. You can select residues in the Workspace and the table by moving the dotted lines to restrict the range of rows and property values. See Plot Toolbar for a description of the toolbar.

Export button

Export the contents of the residue table to a CSV file. Opens a file selector, in which you can navigate to a location and name the file.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

Click Run to analyze the protein structure in the Workspace. When the job finishes, the residue properties are added to the table and the first is plotted.

The Job Settings button opens the Residue Analysis - Job Settings Dialog Box, where you can make settings for running the job.

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. It also displays a progress bar for the job.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

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.

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