How can I retrieve the structure of only one domain from a two-domain protein structure in the alpha Fold database?

Víctor Antonio García-Angulo @Victor-Garcia-Angulo-2

06 September 2024 1 7K Report

I need to perform domain alignments. But I need to compare only one of the domains from a protein. How can I crop the domain from the full structure protein predicted in the alpha fold database?

Raghad Mouhamad

By following these steps, you can effectively isolate a single domain from a two-domain protein structure:

Download the full protein structure from AlphaFold.

Identify the domain boundaries using databases like UniProt, Pfam, or InterPro.

Use PyMOL or similar software to select and extract the domain.

Save the domain as a new PDB file.

Verify the structure before proceeding with alignments.

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