Ligand/Solvent Placement Panel

This panel allows you to place a ligand or solvent molecules in a region that contains an appropriate amount of density, and run a job to optimize the placement.

To open this panel, click Ligand/Solvent Placement in thePrimeX Panel.

  • Overview
  • Using
  • Features
  • Additional Resources

Overview of Ligand/Solvent Placement

Ligand and solvent molecule placement works by docking the molecule with Glide to a protein site that is defined by a region of electron density. This procedure is especially useful if the ligand or the solvent molecule can adopt more than one conformation. Glide performs a rapid conformational search of the most likely conformations, and docks each conformation using SP docking mode. The results are determined by both the standard energetic terms from Glide and the fit to the density, with the fit to the density more highly weighted by default. The best-scoring conformations are returned. Each docked molecule with the protein included is returned as a separate entry.

The density regions are identified by analyzing a difference density map, which must be generated and displayed before you start (see Creating and Displaying Electron Density Maps). Connected density peaks are combined into density “blobs” and listed in a table. The blob is used to define the Glide enclosing box and also the map that is used to fit the ligand. The centroid of the blob is the centroid of the box.

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see primex Command Help and Running PrimeX Tasks from the Command Line.

Using the Ligand/Solvent Placement Panel

To place a ligand or solvent molecule:

  1. Generate a difference density map, and display it in the Workspace.

  2. Open the Ligand/Solvent Placement panel.

    If you do not have a difference density map displayed when you open the panel, you can generate one with the Create Map Panel, then click Update in the panel to analyze the peaks and locate the blobs, or reopen the panel with the map displayed.

  3. Select the source of the ligand or solvent molecule, under Use ligands from.

    • If you selected File, enter the name of the Maestro file that contains the ligands in the File name text box, or click Browse and navigate to the file.
    • If you selected Selected entries, ensure that the desired entries are selected in the Project Table.
    • If you selected Solvent, select the desired solvent molecules in the table.

    You can place multiple molecules in the same density blob, to see which of them fits best. Each molecule is placed in turn into the blob, and the results for each molecule are returned as separate entries. This allows you to compare results for several molecules that might fit into the blob.

    Note: The placement does not attempt to place two molecules into the blob at the same time and optimize their relative arrangement inside the blob. If you want to the blob to contain more than one molecule, it must be done in separate runs, with the blob split into blobs that can accommodate only one of the molecules.

  4. Select the density blob you want to fit the selected molecule to.

    You can select the blob in the Density blobs table or by clicking on the blob in the Workspace.

  5. Set options as desired.

    These include ligand preparation, generation of symmetry mates near the site, and refinement of poses after docking.

  6. Choose Job Settings from the Settings button menu set the job parameters in the Job Settings Dialog Box, and click Run to run the job.

    By default, a variable number of poses is returned, with at least eight poses for every molecule in the input list. Two properties are returned to the Project Table from the job, labeled glide gscore and glide denscore. The first of these is the GlideScore, which is a measure of the ligand binding affinity. The second is a parameter that measures the fit to the density, which is calculated from the sum of the electron density over all atoms in the ligand. In both cases, lower (more negative) values indicate a better fit. The results are ranked and sorted in the Project Table by the denscore. If you selected Refine Poses (see below), only the five best poses over all the input molecules are returned.

When the job finishes, it is useful to perform a rigid-body refinement on the molecule to fine-tune the placement. You can do this in the Reciprocal-Space Refinement Panel.

After placing one set of molecules in a density blob, you can use the results to generate new difference maps using the Create Map Panel, and place other molecules in other blobs.

Ligand/Solvent Placement Panel Features

Use ligands from options

These three options allow you to choose different sources for the ligands to be placed in the selected density blob. You can specify multiple ligands under each option, which allows you to determine which of several possibilities fits best at the given location. The options are:

File

Use ligands from a specified file. When you choose this option, the File name text box and Browse button become available. You can then enter the file name in the text box, or click Browse to navigate to the file in a file chooser.

Selected entries

Use the entries that are selected in the Project Table for the ligands.

Solvent

Use the solvent molecules that are selected in the table below, which lists common solvent molecules. The table columns display the name, PDB ID, and number of atoms in the molecule. You can select multiple rows with shift-click and control-click.

Generate symmetry mates near site option

Select this option to generate crystal mates near the active site. This option is useful if symmetry-related atoms that are part of another protein monomer are close to the active site, and could influence the ligand placement. These symmetry-related atoms are then included in the grid generation for the Glide docking job.

Prepare ligand with LigPrep option

Select this option to run LigPrep on the ligand before placing it. The LigPrep job is run as the first part of the ligand placement job. You must have a LigPrep and an Epik license to use this option. For more information on LigPrep, see the LigPrep Panel topic or the LigPrep User Manual — Contents. The preparation includes generation of ionization and tautomeric states, with retention of the original tautomer and a maximum of 4 structures generated.

Refine poses option

Select this option to run a post-docking real-space minimization of the ligand in the field of the receptor. This option improves the geometry of the docked ligand and the fit to the electron density. When selected, three additional properties related to the real-space refinement are returned to the Project Table:

  • Real-space R-factor.
  • Coverage—This statistic presents the percent of atoms in the ligand covered by electron density when a Fo-Fc map is contoured at 3 sigma.
  • LigandScore—This property is calculated from the other two values, and provides a way of comparing the electron density fit of two different ligands in the same site.

All likely poses are ranked by the real-space R-factor and then the five poses with the best ranking are returned, with no consideration of whether they are the same or different molecules from the input list.

If this option is not selected, a variable number of poses is returned, with at least eight poses for every molecule in the input list. Two properties are returned to the Project Table from the job, labeled glide gscore and glide denscore. The first of these is the GlideScore, which is a measure of the ligand binding affinity. The second is a parameter that measures the fit to the density, which is calculated from the sum of the electron density over all atoms in the ligand. In both cases, lower (more negative) values indicate a better fit. The results are ranked and sorted in the Project Table by the denscore.

Electron density weights text boxes

Enter the weights to be given to the energy and scoring terms in the ligand placement job. The two weights are:

  • Energy—Weight of density terms used to mix into the Coulomb/van der Waals energy. Default:120.

  • Score—Weight of density terms used in the rough scoring function. Default: 50.

The allowed values for both weights range from 1 to 9999.

A weight of 10 produces results that weight the density fit and the molecular interaction terms approximately equally. The larger default values have been optimized to produce poses typical of those found in the Protein Data Bank.

Calculation Settings button

This button opens the Calculation Settings Dialog Box, in which you can set the resolution limit, overall B-factor scaling, choose a bulk solvent correction, set limits for rejecting reflections, and choose whether to include hydrogen atoms in the output. Of particular interest are the settings for the source of the map, which can be taken from a phased reflections file.

Density blobs table

Table of density blobs computed from the peaks in the current difference map, in order of volume. The volume is listed in the table. You can select only one blob at a time. The selected blob is used for placement of the ligand or solvent molecule. When you select a blob in the table, the Workspace view centers on the blob, and the sphere that marks the blob is colored red. When you pick a blob in the Workspace, it is also selected in the table. A box is drawn around the selected blob, which is the enclosing box for Glide, and is also used to generate a map for Glide docking.

If there are several adjacent blobs that might contribute to placed molecule, choose the one that is closest to the center of the desired molecule location. Sometimes decreasing the contour level of the maps (see Surface Manager Panel) can join two blobs into one. After making this adjustment, click Update to obtain the new blob values.

Update button

Recompute the density blobs from the map and update the table. This button is useful if you generate a difference density map after opening the panel, for example, or make changes in the Workspace or the contour level.

Next and Previous buttons

Select the next blob or the previous blob in the table.

Minimum volume to display text box

The value in this text box sets the cutoff for the volume of the blobs that are displayed in the Density blobs table. Blobs with volumes smaller than the value set are not displayed.

Pick blob option

Select this option to pick density blobs in the Workspace. When a blob is picked it is also selected in the Density blobs table. The selected blob is colored red; unselected blobs are green.

Job toolbar

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

The Job Settings button opens the Ligand/Solvent Placement - 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.

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