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[ Pharmacophore Draw 2D | Pharmacophore Draw 3D | Pharmacophore Search | Extract 3D pharmacophore | Color 2D ]
Pharmacophores can be drawn in 2D in the ICM Molecular Editor or in 3D in the Graphical Display. 2D pharmacophore sketches can be used to search chemical tables (spreadsheets) containing 2D or 3D coordinates. A 3D pharmacophore can be used to search chemical tables containing 3D coordinates only.
16.10.1 Pharmacophore Draw 2D |
A 2D pharmacophore can be drawn using the ICM Molecular Editoror if you are going to use the drawing to search it is more efficient if you draw it in the Chemical Search window.
Use the distance bond button and the add pharmacophore group button to sketch the pharmacophore. The distance bond button represents the number of bonds between each pharmacophore point. You can edit the distance by right clicking on the bond and selecting edit. Other groups such as aromatic can be added using the standard molecular editor buttons.
NOTE: Do not mix the 2D and 3D pharmacophore environment. For example do not edit a 3D pharmacophore in the 2D editor. |
16.10.2 Pharmacophore Draw 3D |
The easiest way to begin drawing a 3D pharmacophore is to draw a chemical in the ICM Molecular Editor which contains the key pharmacophore groups you want and then convert to 3D and extract the pharmacophore groups.
To draw a 3D pharmacophore this:
To move a pharmacophore group:
NOTE: Distances between groups can be monitored using the atom distance measurement tool. See Calculating the distance between two atoms. |
To change a pharmacophore group:
To make a new pharmacophore group:
The easiest way to make a new pharmacophore group is to clone a pre-exisiting one. To do this:
To change the direction of a pharmacophore group:
To remove the direction of a pharmacophore group:
16.10.3 Pharmacophore Search |
To perform a pharmacophore search using a 2D pharmacophore:
To perform a pharmacophore search using a 3D pharmacophore:
16.10.4 How to extract a 3D pharmacophore from a ligand. |
16.10.5 How to color a 2D chemical sketch by pharmacophore feature. |
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