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The target defines what the binder should recognize. The binder specification defines what you want to design.

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Use a Boltz specification

In the design form, choose a supported built-in specification such as Boltz Nanobody or Boltz Antibody. You can use these without first creating a custom specification in the project.
Protein design form with available binder specifications

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Use a custom specification

Create a custom specification when you need control over a framework, sequence, structure, or designable regions.
  1. Open the project’s binder specification creation flow.
  2. Name the specification and choose its modality.
  3. Use a supported template, import a PDB structure, upload a structure, or enter sequences as offered by the form.
  4. Select the chains and residues that belong in the binder.
  5. Define the regions the model may design. Keep regions fixed when they must be preserved.
  6. Review any excluded amino acids, motif lengths, and chain assignments.
  7. Create the specification and select it in the design form.
Custom binder specification editor
For antibody-like binders, review the framework and CDR assignments before you create design regions. Use the numbering controls shown in the editor rather than assuming that file residue numbers equal sequence positions. Available specifications depend on the project and organization. Select a specification that the current design form accepts. See Run protein design.