Shape Screening Settings Dialog Box

In this dialog box you can select a variety of options to control the process and results of a shape screen. Only a few options are available for screening on a GPU; these are marked in the descriptions below.

To open this dialog box, click Screening Settings in the Shape Screening Panel.

  • Features
  • Additional Resources

Shape Screening Settings Dialog Box Features

Only a few options are available for screening on a GPU (image on right); these are marked in the descriptions below.

 

Generate conformers option

Select this option to run a conformational search for the molecules being screened, using ConfGenX. This option is not needed if the input molecules already consist of conformer sets. It is off by default if you choose to screen a Phase database, but you can turn it on if the database does not contain conformers or if you want to generate conformers anyway.
(Sets -flex for shape_screen Command Help.)

Target number of conformers text box

Enter the target number of conformers per input molecule to be generated in this text box. Default: 50.

Filter out ligands with similarity below option and text box

Filter out ligands whose similarity to the query is lower than the value given in the text box. The allowed range is 0-1. Available for GPU screening.
(Sets -filter forshape_screen Command Help.)

Create Phase subset file from hits option

If you are searching a Phase database, select this option to create a Phase database subset from the matches to the query.
(Sets -osub for shape_screen Command Help.)

Score in place option

Select this option to compute similarities without aligning the molecules to the queries. Available for GPU screening.
(Sets -scoreInPlace for shape_screen Command Help.)

Screen a subset only option, text box, and Browse button

If screening a Phase database, screen only the specified subset. Enter the full path to the Phase database subset file in the text box, or click Browse and navigate to the database subset file. The file must end in _phase.inp.
(Sets -isub for shape_screen Command Help.)

Sort output structures by decreasing similarity option

Select this option to sort the output. By default the output is not sorted. The sort takes about 2K of memory per output structure. The limit on the number of output structures is given in the Maximum number of structures to save text box; by default it is 10000, which corresponds to about 20MB memory used for the sort.
(Sets -sort for shape_screen Command Help.)

Maximum number of structures to save text box

Limit the number of structures to save when sorting by decreasing similarity to the value given in this text box. The default is 10000. Available for GPU screening.
(Sets -keep for shape_screen Command Help.)

Similarity normalization option menu

Choose a scheme for normalizing the similarity. The similarity is defined by Sim(A,B) = O(A,B)/f[O(A,A),O(B,B)], where O is the overlap between the query A and a molecule B that is being screened. The function f can be one of four choices, which are given on the option menu:

  1. Maximum—Normalize to the maximum of O(A,A) and O(B,B)
  2. Minimum—Normalize to the minimum of O(A,A) and O(B,B)
  3. Query structure—Normalize to O(A,A)
  4. Screen structure—Normalize to O(B,B)

Note that using any scheme other than the first can yield similarities larger than 1. Available for GPU screening.
(Sets -norm for shape_screen Command Help.)

Customize atom weights option and section

Customize the weights used for contributions from individual atoms when evaluating the volume score for typed or untyped atoms. This is useful for emphasizing or de-emphasizing chosen parts of the reference structure in the score. These options are only available if the reference conformation is sampled, and the scoring is done on typed or untyped atoms.

Default atom weight option menu and Apply button

Choose the default value for the weights from the option menu. The values are between 0.0 and 1.0; the default is 1.0. Click Apply to set the default weights to the chosen default weight).

Get Workspace Selection button

Select the rows in the table for the atoms that are selected in the Workspace (reference) structure.

Custom weight option menu and Apply button

Set the weights for the atoms in the selected rows of the weights table to the chosen value, when Apply is clicked. The default is 1.0.

Weights table

This table lists the atoms in the Workspace structure by atom number and element (and PDB name if it exists), and the weight to use for each atom. You can select multiple rows to set the weight value, using the tools above the table. The atoms in the selected rows are highlighted in the Workspace. The weights are applied in the alignment, but are not stored.

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