The Protein Optimizer

The Protein Optimizer (Image optimize_protein_16_n_p) makes it possible to modify protein side chains while taking surrounding molecules into account.

It can be used to replace missing atoms in a protein structure, to refine the results of modeling from the Find and Model Structure tool (Find and Model Structure), or to investigate how mutations in a binding pocket may affect binding.

To invoke the Protein Optimizer dialog, click the Protein Optimizer button in the Structure tools panel below the Project Tree. Then select a residue to be changed.

Note: It is possible to undo and redo operations done while using the dialog. If the dialog is canceled, all changes done are rolled back.

Also note: If multiple mutations are desired, it is best to make them with the Find and Model Structure tool, which will usually give more accurate results (see Section 10.10.6 for details). The output of Find and Model Structure may then be refined in the Protein Optimizer.

The Protein Optimizer dialog (figure 10.27) is composed of the following five panels:

  1. The selection panel shows the protein and residue currently being optimized.
  2. The issues panel lists any chemical issues for the current residue.
  3. The modify residue panel performs modifications on the current residue.
  4. The modify surrounding residues panel performs modifications on a local region of the protein.
  5. The visualization panel controls the view.

Image proteinOptimizerDialog
Figure 10.27: The Protein Optimizer dialog



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