Protein Design, accessed through Protean 3D, lets you make one or more changes at the residue-level on a protein structure, and calculates whether these changes are likely to be stabilizing or destabilizing compared to the original structure. Two workflows are available: Create specific variant and Scan for hotspots that provide stability. Variant calculations are performed for one residue at a time, not for groups of residues as a single unit. Note that Protein Design is not suitable for use in modeling changes involving indels. For indels, we recommend adding or removing amino acids from the sequence and submitting the edited sequence as a query for NovaFold.
The Protein Design wizard consists of five consecutive wizard screens, each described in a separate topic:
To launch the Protein Design wizard, choose one of the following commands. Some commands let you launch the wizard with the workflow pre-selected and the Substitutes table already pre-populated.
| Command | Opens Wizard at | Workflow screen selection | Substitutes screen pre-populated with: |
|---|---|---|---|
| File > New Protein Design Prediction | Workflow screen | None | Nothing |
| Modeling > Protein Design > New Protein Design Prediction | Workflow screen | None | Nothing |
| Modeling > Protein Design > Create Variant With > Selection | Substitutes screen | Create specific variant workflow | Selected sequence range |
| Structure > Create Variants or right-click on a selected range in the Analysis or Sequence view and choose Create Variants | |||
| Modeling > Protein Design > Create Variant With > Document | Substitutes screen | Create specific variant workflow | Entire sequence range |
| Modeling > Protein Design > Scan for Hot Spots With > Selection | Substitutes screen | Scan for hotspots that provide stability workflow | Selected sequence range |
| Modeling > Protein Design > Scan for Hot Spots With > Document | Substitutes screen | Scan for hotspots that provide stability workflow | Entire sequence range |
For additional shortcuts, see The Welcome Screen.
Tools available in the Protein Design wizard:
The following tools are available in the bottom left corner of each Protein Design wizard screen:
- To display the help for this topic, press the question mark icon (
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).
).- To enter an NCBI Access ID, press the Set Access ID (
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) tool. This causes the Access ID dialog to pop up. See Access ID dialog for information.
) tool. This causes the Access ID dialog to pop up. See - To submit an idea for a new feature, press the Suggest a feature (
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) tool.
) tool.- To view information about your service plan, press the Show Service Plan (
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) tool. For sequence or text search services, the ensuing dialog describes the state of your service plan and any warning or error text messages. The license control has three states: Active, Expiring, and Expired.
) tool. For sequence or text search services, the ensuing dialog describes the state of your service plan and any warning or error text messages. The license control has three states: Active, Expiring, and Expired.
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