Optimize Sequence Alignment at Binding Site Dialog Box
Optimize the alignment at the binding site after a full sequence alignment. The optimization removes gaps in the secondary structure in the specified binding site region.
To open this dialog box, click the Optimize button in the Build Homology Model Panel.
- Features
- Additional Resources
Optimize Sequence Alignment at Binding Site Dialog Box Features
- Use option menu
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Choose an item to identify the binding site.
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Ligand or cofactor—define the binding site as residues that are in proximity to the chosen ligand. The ligands and cofactors identified in the template are listed on the menu. The Binding site radius text box is available if you choose a ligand or cofactor.
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Selected Residues—use the selected residues to identify the binding site. You must select residues in the template before opening this dialog box; if they are not selected, close the dialog box and select them, then reopen it. The selected residues are listed below the menu
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- Binding site radius text box
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Specify the radius of the binding site. Residues that have any atom within this distance of any atom in the ligand or cofactor are included in the binding site. Only present if you choose a ligand or cofactor from the Use option menu.