Clustering TM domain of transmembrane protein

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    • March 22, 2010 at 6:26 am #487
      Anonymous

        Hi,

        I have a trouble when clustering decoys of a transmembrane protein.

        I use the MembraneAbinitio protocol to generate 5,000 decoys. Now I attempt to cluster them only considering the trans-membrane segments because my target protein has a very large (120 residues) cytoplasmic domain.
        I notice that there is an option for clustering– “exclude_res”. I wonder how this option works? As you can see, I have more than 120 residues to exclude?

        Anyone can help me?

        Thank you a lot!

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