Specify Receptor Dialog Box

Specify Receptor Dialog Box Features

 

• Receptor file name text box and Browse button
• Use Selected Project Table Entry button
• Minimum H-bonds required box
• Preserve specific H-bonds option and section
  • Pick H-bonds to preserve option
  • Require all N critical (red) H-bond matches text box
  • Require M of N optional (blue) H-bond matches option and boxes
• Require new H-bonds option and section
  • Pick new H-bonds to require option
  • Require all N critical (red) H-bond matches text box
  • Require M of N optional (blue) H-bond matches option and boxes
• Prevent heavy-atom steric clashes with receptor option and section

Receptor file name text box and Browse button

Click Browse to navigate to and select a Maestro file that contains the receptor. The file name is displayed in the text box, which is noneditable.

Use Selected Project Table Entry button

Use the selected entry in the Project Table for the receptor. There must be only one entry selected in the Project Table.

Minimum H-bonds required box

Specify the minimum number of hydrogen bonds to the receptor that are required for a new core. This general minimum is useful for ensuring good binding to the receptor, and new cores that form hydrogen bonds to the receptor that are absent in the template (if you do not want to specify these hydrogen bonds in advance).

Preserve specific H-bonds option and section

Select this option to require specific H-bonds to the receptor from a new core that exist between the template and the receptor. The existing H-bonds are marked as arrows between the template and the receptor.

Pick H-bonds to preserve option

Select this option to begin picking H-bonds in the Workspace. The first click marks the H-bond as an optional match (blue), the second marks it as a required match (red), and the third returns it to the unmarked state (yellow). When you have finished selecting H-bonds, deselect this option. The count of required and optional matches is updated.

Require all N critical (red) H-bond matches text box

This noneditable text box displays the number of "critical" matches.

Require M of N optional (blue) H-bond matches option and boxes

Require a minimum number of matches to any of the optional matching H-bonds. The total number of such H-bonds that you selected is displayed in the noneditable text box. You can set the minimum number in the other box.

Require new H-bonds option and section

Select this option to require specific H-bonds to the receptor from a new core that do not exist between the template and the receptor. Potential new H-bonds are marked on the receptor acceptor and donor atoms.

Pick new H-bonds to require option

Select this option to begin picking H-bonds in the Workspace. The first click marks the H-bond as an optional match (blue), the second marks it as a required match (red), and the third returns it to the unmarked state (yellow). When you have finished selecting H-bonds, deselect this option. The count of required and optional matches is updated.

Require all N critical (red) H-bond matches text box

This noneditable text box displays the number of "critical" matches.

Require M of N optional (blue) H-bond matches option and boxes

Require a minimum number of matches to any of the optional matching H-bonds. The total number of such H-bonds that you selected is displayed in the noneditable text box. You can set the minimum number in the other box.

Prevent heavy-atom steric clashes with receptor option and section

Select this option to filter out cores in which too many heavy atoms clash with receptor heavy atoms, and set criteria for these clashes.

Maximum clashing ligand atoms box

Specify the maximum number of ligand atoms that are permitted to clash with the receptor in this box. It is not always necessary to exclude all clashes, because of the flexibility of both the receptor and the ligand.

Clash criterion: less than N Å box

Specify the distance inside which atoms are considered to clash.