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Define the system

Choose target components and copies that represent the system you want to study. Review the structural construct and the intended interface before completing target setup. Check residue numbering and chain identity whenever you import a structure or transfer selections between sources.

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Choose deliberate requirements

Use the available binding and structural guidance to express the biological question. Add a requirement only when you can explain its purpose. Choose binder specifications that fit your modality. Use custom specifications when you need control over fixed and designable regions. For antibody-like binders, check framework and CDR assignments.

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Review the run settings

Choose the size or effort controls offered for the selected target based on its difficulty and your available resources. A large search does not guarantee a particular number of useful candidates.

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Evaluate the result

Inspect the interface and review relevant confidence and sequence properties. Use tags to group candidates by scaffold, binding region, or hypothesis. Include diverse candidates in a shortlist when that helps test your question. Confirm binding, specificity, and functional activity with experiments. See Results and Triage.