Predict Side Chains Panel

Predict the conformation of side chains in one or more proteins by sampling orientations to minimize the energy. The sampling can include the orientation with respect to the backbone, and sampling of the backbone as well. The sampling can be run with periodic boundary conditions, in implicit solvent, and with an implicit membrane.

For technical details about side-chain prediction, see Side-Chain Prediction Technical Details.

To open this panel, click the Tasks button and browse to Protein Preparation and Refinement → Predict Side Chains.
To open this panel from the entry group for the results of a homology modeling job, use the Workflow Action Menu .

  • Using
  • Features
  • Additional Resources

Using the Predict Side Chains Panel

When selecting residues for side-chain prediction, you might want to use the Atom Selection dialog box, which provides proximity options that allow you to select all residues within a certain distance of a ligand, for example.

If you imported a PDB structure that has residues with missing atoms, you can select those residues by clicking Select Residues with Missing Atoms. The selection is based on the information generated when the structure was imported, and does not use the current structural information. The selection therefore includes any residues that were fixed since import.

If you are refining a homology model, you should consider refining residues whose side-chain coordinates did not come from the templates. These are residues for which the Homology Status is equal to 1 and 2. The backbone coordinates for residues with a Homology Status of 1 were taken from the templates, but not the side chain coordinates. For residues with a Homology Status of 2 (none of the coordinates came from the templates), you should consider doing a loop refinement first. You can select all residues with non-template side chains by clicking Select Non-Conserved Residues.

If heavy atoms are added to a residue because they were missing, a boolean property side chain added (b_psp_side_chain_added) is added to all atoms in the residue. You can use this property to select these side chains for other tasks, such as minimization.

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 prime Command Help and prime—Build and Refine Protein Structures.

Predict Side Chains Panel Features

Use structures from option menu

Choose the structure source for the current task.

  • Project Table (selected entries)—Use the entries that are currently selected in the Project Table.
  • Workspace (included entry)—Use the entry that is currently included in the Workspace. Only one entry must be included in the Workspace.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
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.

Solvation model option menu

Choose a continuum solvation model for the refinement. The choices are:

  • VSGB—Use the variable-dielectric generalized Born model, which incorporates residue-dependent effects. The solvent is water.
  • Vacuum—Do not include solvation.
  • Chloroform—Use chloroform as the solvent, modeled with the Surface Generalized Born (SGB) method.
Force field option menu

Choose the force field for the current task. The choices are OPLS_2005 and OPLS4. The default is OPLS4 if it is available, otherwise it is OPLS_2005, unless you set the default in the Force Field settings section of the Preferences Panel.

Use customized version option

Use your customized version of the OPLS4 force field, rather than the standard version in the distribution. Only available when you choose OPLS4 from the Force field option menu and you have the appropriate license. This option is set by default to the value of the Use custom parameters by default option in the Preferences panel, under Jobs - Force field, when the current panel is opened. The default directory for the customized version can also be specified as a preference, in the same location.

If the customized version is missing or invalid, the text of this option turns orange and an orange warning icon is displayed to the right, with a tooltip about the problem.

Parameter set button

Select the set of custom parameters for the OPLS4 force field. Opens the Set Custom Parameters Location Dialog Box. Only available when you choose OPLS4 from the Force field option menu and you have the appropriate license.

Residues for side chain refinement picking tools

Select the residues for side-chain refinement using the standard picking tools.

Select Residues with Missing Atoms button

Select residues from an imported PDB structure that have missing atoms. The selection is based on the information generated when the structure was imported, and does not use the current structural information. The selection therefore includes any residues that were fixed since import. This button is displayed when you select Predict side chains from the Task menu.

Select Non-Conserved Residues button

Select residues from a homology model whose side chain coordinates were not derived from the templates. The atoms in these residues have a Homology Status property of 1 or 2.

Sampling algorithm option menu

Choose a sampling algorithm that allows for orientational changes and backbone movement. These algorithms are primarily aimed at cases where some degree of backbone sampling is likely to be required, such as in homology modeling or cross-docking, where the backbone conformation of the initial structure might not be entirely correct. These methods allow for progressively more backbone movement during the side-chain prediction calculations.

While these algorithms can be run on any arbitrary set of residues in a given structure, the general intent is that they should be run on a relatively small subset of the structure, such as a binding site or other region of interest. Running these calculations on an entire structure is likely to result in more structural changes than were intended. For example, since the CA-CB sampling method involves a minimization of all residues being predicted, using this method on the entire structure results in minimization of the entire structure in the final stage, which is generally undesirable.

The option menu has these choices:

  • Default—Use the default algorithm, which varies only the side chains and keeps the alpha and beta carbons fixed.
  • Monte Carlo—Perform Monte-Carlo sampling of side-chain conformations. When this algorithm is selected, the Maximum number of structures to return option and text box becomes available.
  • With CA-CB vector sampling—In addition to the default algorithm, vary the orientation of the CA-CB bond by up to 30°.
  • With backbone sampling—In addition to the default algorithm, perform a loop prediction on three residues: the residue whose side chain is being predicted and the residue on either side.
Maximum number of structures to return option and text box

Select this option to return more than one conformation of the side chains, and specify the number of conformations to return in the text box. Only available for Monte Carlo sampling.

Constraints button

Open the Predict Side Chains - Constraints Dialog Box, to set up distance (atom-pair) and Cartesian (initial position) constraints.

Options button

Open the Predict Side Chains - Options Dialog Box to set up options: use of an implicit membrane and crystal symmetry, the solvent dielectric constant, the random seed for side-chain prediction.

Job toolbar

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

The Job Settings button opens the Predict Side Chains - 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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