Protein structure alignment
The Align Protein Structure tool allows you to compare a protein or binding pocket in a Molecule Project with proteins from other Molecule Projects. The tool is invoked using the (
) Align Protein Structure action from the Molecule Project Side Panel. This action will open an interactive dialog box (figure 10.14). By default, when the dialog box is closed with an "OK", a new Molecule Project will be opened containing all the input protein structures laid on top of one another. All molecules coming from the same input Molecule Project will have the same color in the initial visualization.
|
Note! Care should be taken when using the Setup Binding Site tool on a Molecule Project containing a structure alignment. This is because, by default, all the protein chains lying on top of each other will be included in the setup. Make sure to un-select those protein chains in the Binding Site Setup dialog box that should not be included in the Binding Site Setup. |
Subsections
- The Align Protein Structure dialog box
- Example: alignment of calmodulin
- The Align Protein Structure algorithm