Prime User Manual - ISP

Chapter 9: Docking Covalently Bound Ligands
When you are satisfied with the SMARTS pattern, you must then designate an atom on the
ligand that is removed, along with the atoms attached to it, when the ligand forms a bond with
the receptor. The fragment with the smaller number of atoms is the part that is removed. The
atom is specified by its index (position) in the SMARTS pattern; the first atom index is 1. This
index must be entered into the Leaving atom text box.
Having defined a SMARTS pattern and the leaving group, click Add. The SMARTS pattern is
added to the table below, and will be used when processing the ligands. You can repeat this
process for as many SMARTS patterns as you want to use. If you want to remove a pattern
from the table, select it and click Remove.
9.1.3 Specifying the Receptor Bond to Break
In the Receptor options section you specify the bond in the receptor that is broken to form a
bond with the ligand. The receptor must be displayed in the Workspace, and is written to a file
when you start the job.
To define the bond that is broken, select Pick receptor bond to break, and pick the desired bond
on the receptor in the Workspace. The Staying atom and Leaving atom text boxes are filled with
the atom numbers of the atom in the bond that remains and the atom in the bond that is
removed when the bond is broken. The bond is marked in the Workspace with yellow markers.
If you pick the wrong bond, you can simply pick again, and the new bond replaces the old.
You can also enter or edit the atom numbers in the Staying atom and Leaving atom text boxes.
To ensure that you have the correct atom numbers, you should label the atoms. For more information
on labeling atoms, see Section 6.3 of the Maestro User Manual.
9.1.4 Specifying Receptor Residues to Sample
In the Receptor options section you can also choose residues that are allowed to adjust to the
formation of the covalent complex in the loop sampling procedure.
The first choice is whether to sample the residue that is attached to the ligand. To do so, select
Sample attachment residue.
The next step is to pick other residues in the Workspace for sampling. To do so, select Pick
additional residue to sample, and pick residues in the Workspace. You can pick any number of
residues. As well as picking, you can select the desired residues in the Atom Selection dialog
box, which you open by clicking Select. The residues that you select by either method are
listed in the Additional residues text box.
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