VSW - Docking Options Dialog Box

VSW - Docking Options Dialog Box Features

The features and default values in this dialog box depend on whether it was opened for HTVS, SP, or XP docking. Restrictions on any feature are noted in the feature description.

• Generate multiple input conformations option
• Docking method options
• Perform post-docking minimization option
• Apply strain correction terms option
• Use selected constraints for each grid option
• Generate up to N poses per compound state text box
• Write XP descriptor information options
• After docking, keep options
• Retain options

Generate multiple input conformations option

Run a MacroModel conformational search job on the input structures corresponding to the best poses from the previous stage to locate the lowest-energy conformer, using two different force fields. This option generates two extra input structures for XP docking, and therefore takes several times as long as an XP docking run with a single structure (including the conformational search). The variations in the input structures often produce better final results.

Docking method options

There are two options that are common to all stages for the docking method, Dock flexibly and Dock rigidly. For SP and XP docking you can choose from two more options, Refine and Score in place. These options are described more fully in the Ligand Docking Panel DEPRECATED topic.

Under Dock flexibly, you can choose a treatment of amide bonds conformations from the Amide bonds option menu:

• Vary amide bond conformation—Allow non-planar conformations, without a particular penalty.
• Allow trans conformation only—Filter out amide bond conformations that deviate from trans by more than 20°.
• Retain original amide bond conformation—no variation of the conformation is permitted.
• Penalize non-planar conformation—Apply a penalty to nonplanar amide bonds.

Perform post-docking minimization option

This option allows you to perform a minimization of the poses following the final docking, and can be used for both flexible and rigid docking. The minimization optimizes bond lengths and angles as well as torsional angles, and rescores the poses using the scaled Coulomb-van der Waals term and the GlideScore.

Apply strain correction terms option

Apply strain correction terms in the final scoring. These terms are evaluated by optimizing each ligand pose as a free ligand, first with constraints on all torsions, then without these constraints. The difference is used to compute a penalty term for unreasonably high strain.

Use selected constraints for each grid option

This option enables you to apply the constraints that you selected for each grid.

Generate up to N poses per compound state text box

Enter the number of poses per compound state to generate. This limit restricts the final results if you choose to retain all good scoring poses.

Write XP descriptor information options

Select this option to write out XP descriptor information. This feature requires a license to use it. If you select this option, you can also choose to dock a fragment library that enables the maximum values of XP descriptors to be calculated, and you can choose to apply the selected constraints to the docking of these fragments.

After docking, keep options

These two options allow you to specify the percentage (upper text box) or number (lower text box) of the best compounds to keep. A compound may consist of several ionization or tautomeric states.

Retain options

This option menu allows you to choose how many ionization or tautomeric states to keep for each compound:

• Only best scoring state (default for XP)
• All good scoring states (default for SP)
• All states (default for HTVS, not available for XP)

The rationale for keeping all ionization and tautomeric states is that the actual state that scores best can vary with the accuracy level. Keeping all states of a particular compound in the early stages ensures that the structures that score best in later stages are not discarded.