R-Group Viewer Panel

R-Group Viewer Panel Features

 

• Input Structures section
  • Structure display controls
  • Structure display area
• R Groups section
  • Restrict visible input structures by selecting R-groups option
  • Positional combining rule options
  • Select All R-Groups, All Positions button
  • Export Input Structures button
  • Export R-Group Structures button
  • R-group table
• Attachments table
• Analysis buttons
  • Activity Cliffs button
  • Importance Analysis button
  • Heat Map button
  • Pharma RQSAR button
  • E-State RQSAR button
  • SAR Table button

Input Structures section

In this section of the panel, you can view the individual input structures, annotated to display the attachments to the core.

Structure display controls

These controls allow you to choose which of your input structures to display. The arrow buttons can be used to step through the structures. The current structure number is displayed in the text box. You can edit the text box to display a particular structure.

Structure display area

This area displays the structure as a 2D image. The attachment points are marked with arrows pointing towards the R group. The arrows are color-coded to match the rows in the Attachments table. The arrow is outlined for the current attachment, which is the attachment that is selected in the Attachments table, and whose R groups are displayed in the R Groups section.

R Groups section

In this section of the panel you can view the R groups for a given attachment position, and restrict the structures that are shown by selecting R groups. You can also export the structures or the R groups.

Restrict visible input structures by selecting R-groups option

Restrict the structures that are displayed in the Input Structures section by selecting the R groups at each position that you want to display. By default, all R groups (fragments) are selected. For each position you can select the desired R groups in the table. To change the position whose R groups are displayed, select the position in the Attachments table.

Positional combining rule options

Select an option for combining the selections at each position.

• AND—Display only those structures that have a selected R group (fragment) at all attachment positions.
• OR—Display only those structures that have a selected R group (fragment) at one or more of the attachment positions.

Select All R-Groups, All Positions button

Select all R groups for each of the attachment positions.

Export Input Structures button

Export the input structures. Opens the Export Input Structures dialog box, in which you can make the following choices:

• Export the structures to a file or to the Project Table.
• Export all structures or only the visible structures (those that are subject to the selection restrictions).
• Superimpose the structures by aligning the cores to that of the first input structure.

The allowed file types are Maestro (.mae, .maegz), SD (.sdf), and SMILES (.smi); the file type written is determined by the extension that you provide for the file name. If the structures are exported to a Maestro file or to the Project Table, the annotations that identify the attachment points are kept; otherwise they are discarded.

Export R-Group Structures button

Export the R groups as separate molecules, capped with methyl groups, to a set of Maestro files or to the Project Table. A dialog box opens to provide information for the export. The R groups at each position are exported to a separate file or an entry group. The base name of the file or the entry group is given in the Filename text box. To this name is added the suffix _rga-N, where N is the position number. This name is used for the entry group name, and the .mae extension is added to it for the file name. The titles of the structures are set to R-group M, where M is the index of the R group.

You can also choose to export the CSV output file if you ran a Canvas MCS calculation to define the core, by selecting Save MCS .csv output.

R-group table

This table displays the 2D structures of the R groups at the current attachment position. The bond that connects an R group to the core is colored the same way and oriented in the same direction as the attachment bond in the input structure. The table cell for the R group that is displayed in the Input Structures section is outlined in black. When you pause the pointer over the table cell, an enlarged image of the R group is displayed. You can select cells in the table when restricting the visible input structures.

Attachments table

This table lists the attachment positions that were located in the analysis. The first column is an index and is color-coded to match the positions marked in the Input Structures display area. Selecting a table row populates the table in the R Groups section with the R groups found at that attachment position. The table is noneditable. The other columns in the table are:

Attachment name	Name given to the attachment on the core-containing structure.
No. of structures	Number of R groups selected at this attachment position. If it is less than the total number at the position, it is shown as selection/total.
Collection file	Name of the collection file created for this attachment point. This is a temporary file.

Analysis buttons

These buttons open panels that display analyses of the properties of the R groups.

Activity Cliffs button

Display a plot of structure differences against property differences of the R groups. Opens the R-Group Analysis — Activity Cliffs Panel.

Importance Analysis button

Display information on the range of properties of the R groups at each position. Opens the R-Group Analysis — Importance Analysis Panel.

Heat Map button

Display a heat map of properties of the R groups. Opens the R-Group Analysis — Heat Map Panel.

Pharma RQSAR button

Set up and generate a QSAR model for the R groups based on pharmacophore feature counts. Opens the Pharma RQSAR Panel.

E-State RQSAR button

Set up and generate a QSAR model for the R groups based on counts of E-state atom types. Opens the E-State RQSAR Panel.

SAR Table button

Display a table of properties of structures as a function of R group. Opens the R-Group Analysis — SAR Table Panel.