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Clustering TM domain of transmembrane protein

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Clustering TM domain of transmembrane protein
#1

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!

Sun, 2010-03-21 23:26
justin