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Ligand Docking — Core Tab |
In this tab you can specify the core of a reference ligand, and use it to perform core RMSD measurements of docked ligand poses or to restrict docked poses to those that lie within some RMSD tolerance of the reference core.
The Core pattern comparison controls allow you to choose which task to use the core definition for:
Select this option to use a core definition for comparison or constraint. This option is off by default. When you select this option, the rest of the options in the tab are enabled.
Use the core definition for computing the RMSD from the reference ligand, but not for docking.
Restrict the docking of ligands so that the ligand "core" lies within a given RMSD of the core in the reference ligand. The core is defined in terms of a set of atoms or a SMARTS pattern; if the ligand does not contain these atoms, it can be skipped. You can enter a tolerance for the RMSD in angstroms for restricting the docking to the reference position in the Tolerance text box.
In this section you can define the core of the reference ligand. These controls become available when you choose Use for RMSD calculations only or Restrict docking to reference position.
This option allows you to pick the molecule to use for the core. The molecule is marked in purple in the Workspace if Show markers is selected. It is automatically selected when the controls in this section become available. It is automatically deselected if you choose SMARTS pattern. You must pick a core-containing molecule before you can proceed to define the core atoms.
This option displays markers for the core-containing molecule and for the SMARTS pattern and RMSD subset atoms, as appropriate. It is selected by default, as there is no other indication of the picked atoms or molecules.
There are three options for defining the core atoms. The first two, All heavy atoms and All atoms, select these atoms from the picked core-containing molecule as the core. The third option, SMARTS pattern, allows you to define the core atoms in terms of a SMARTS pattern. You can pick atoms in the Workspace and click Get From Selection to define the SMARTS pattern, or you can type a SMARTS pattern into the text box. The atoms in the core-containing molecule that match the pattern are marked in the Workspace with green markers. You can also define a subset of these atoms with which to evaluate the RMSD by selecting Pick RMSD subset atoms, then picking the atoms. A lock symbol appears next to the atoms you pick. The RMSD atoms are used both when calculating only the RMSD and when restraining the core: it is the RMSD of these atoms that must fall below the prescribed tolerance in the latter case.
When this option is selected, if a ligand does not match the core pattern it will not be docked. This option is selected by default. If it is deselected, ligands that do not match are docked, but the RMSD with the core is not calculated.
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