Prime User Manual - ISP

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Chapter 9: Docking Covalently Bound Ligands
Prime 2.1 User Manual
Figure 9.1. The Covalent Docking panel.
9.1.2 Defining the Ligand Reactive Groups
In the Ligand reactive groups section, you specify the reactive groups on the ligands, in which
a bond is broken to form a bond with the receptor. Each group is specified by a SMARTS
pattern and the index of the atom that leaves, with its attachments, when the ligand bond is
broken. You can specify multiple reactive groups. For each ligand, all groups are tried for a
match to the ligand, and each match is docked.
To define each SMARTS pattern, you can enter the pattern in the SMARTS pattern text box, or
you can select atoms on a typical ligand molecule in the Workspace, and click Get From Selection
to place a pattern in the SMARTS pattern text box. You can then edit the SMARTS pattern
in the text box if you want.