Isosteric Matching Advanced Options Dialog Box

In this dialog box you can set options for the isosteric matching (shape-based core-hopping) method, to control the atom matching, the similarity of the cores and the alignment of the attachment bonds.

To open this dialog box, click Advanced in the Isosteric Matching panel.

  • Features
  • Additional Resources

Isosteric Matching Advanced Options Dialog Box Features

Shape-similarity atom typing option menu

Choose the types of atoms between which volume overlaps will be calculated. Volume overlaps are computed between atoms that have the same atom type as defined by the choice of atom typing scheme below.

  • None—Don't distinguish different types of atoms when calculating volume overlaps: all atoms are treated the same.
  • MacroModel—Calculate volume overlaps only between atoms that have the same MacroModel atom type.
  • Elements—Calculate volume overlaps only between atoms of the same element.
  • Pharmacophore—Calculate volume overlaps between atoms that have the same pharmacophore type (Acceptor, Donor, etc.) as defined for Phase QSAR models.
Attachment-bond weight box

Set the weights for the atoms in the attachment bonds. The allowed weight range is from 0 to 1. The default is 1.0.

Non-attachment weight box

Set the weights for the atoms in all atoms other than those in the attachment bonds. The allowed weight range is from 0 to 1.The default is 0.2.

The default value produces results in which the cores might not overlap very well. Increasing the non-attachment weight should increase the similarity of the cores, somewhat at the expense of the attachment bonds. For example, increasing the non-attachment weight to 0.7 should yield new cores that are similar to the template core.

Maximum angle deviation box

Maximum deviation of the direction of the attachment bonds on the new core from the corresponding attachment bonds in the template. The angle is the angle between the attachment bond vectors. Smaller values will improve the alignment of attachment bonds.

Maximum distance deviation box

Maximum allowed distance between corresponding attachment bond atoms. Smaller values favor attachment bonds of the same length as in the template.

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