Binding Surface Area Analysis Panel

Compute the change in solvent-accessible surface area upon binding for receptor-ligand pairs. The surface areas and their changes on binding are broken down into contributions from pharmacophore types, residue types, and structural features.

To open this panel: click the Tasks button and browse to Structure Analysis → Binding Surface Area Analysis.

  • Using
  • Features
  • Additional Resources

Using the Binding Surface Area Analysis Panel

The surface area analysis calculates the solvent-accessible surface area of the receptor-ligand complex (the "bound" surface area), the receptor on its own and the ligand on its own (the "unbound" surface areas"), and then calculates the difference in surface area between the bound complex and the unbound receptor and ligand (the "delta" surface area). No changes are made to the structures, so relaxation on binding is not included in the calculations.

The surface areas and the change in surface area are reported as Maestro properties, along with an analysis of the surface area into contributions from pharmacophore types, residue types, and structural features, as well as contributions from specified residues. The table below describes these properties. In this table, entry can be receptor or ligand, and state can be bound, unbound, or delta.

Property type Property names Description
Full SASA sasa receptor full, sasa ligand full Total SASA of all receptor atoms or ligand atoms.
Total SASA sasa entry total state Total SASA of all the receptor atoms or ligand atoms within the system defined by the cutoff value, in the specified state.
SASA by pharmacophore type sasa entry type state Total SASA in the specified state of all receptor or ligand atoms within the system that are of each of the six basic types: hydrophobic, aromatic, donor, acceptor, positive, negative (the values of type). Those atoms not matching any of the types are classified as the type "other".
SASA by residue type sasa receptor pdbname state Total SASA of all receptor atoms within the system that are of a given residue type, for the specified state, identified by the PDB residue type: ala, arg, asp, etc.
SASA by residue sasa receptor residue state SASA of all atoms of specific residues in the given state, identified by the name of the residue.
SASA by structural feature sasa receptor feature state Total SASA of all receptor atoms within the system that are in the backbone, the side chains, helices, loops, or strands. Here, feature can be backbone, sidechain, helix, loop, or strand.

Binding Surface Area Analysis Panel Features

Use structures from option menu

Choose the structure source for the surface area analysis. The structures must either be a set of receptor-ligand complexes or a receptor followed by a set of ligands ("pose viewer file").

  • 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.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
Open Project Table button

Open the Project Table panel, so you can select the entries for the structure source.

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.

Surface area definitions options

Choose an option for the part of the receptor surface to calculate:

  • Calculate surface area for receptor atoms N angstroms from ligand—Calculate the surface area from atoms that are within the specified distance from any ligand atom.
  • Calculate surface area for full receptor—Calculate the entire surface area of the receptor.
Structure information options

Select an option for the inclusion of SASA decomposition for structural features of the receptor.

Include structure output for receptor option

Include information on the surface area and changes for the receptor backbone and side chains.

Include secondary structure output for receptor option

Include information on the surface area and changes for secondary structure elements (helices, loops, strands).

Residue specification section

Specify residues for a breakdown of the surface area and its changes by residue.

ASL pattern text box, Get from Selection button, and Add button

Specify residues by an ASL pattern. Enter an ASL pattern in the text box to specify residues, or select residues in the Workspace and click Get from Selection to create the ASL pattern. Click Add to add the residues from the ASL pattern to the residues table. See Atom Specification Language for more information.

Chain ID text box, Residue number text box, and Add button

Specify residues by chain and number. Enter the chain ID and residue number in the text boxes, and click Add to add the residue to the residue table.

Residue table

Lists the residues that have been selected for the per-residue analysis. The table cells are noneditable.

Clear Residues button

Clear all the residues from the table.

Job toolbar

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

The Job Settings button opens the Binding Surface Area 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.

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.

Related Topics