how to pick fragments for a transmembrane protein

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    • #1286

        Dear all,

        I have created fragments with script using the following command lne: -verbose -nosam -nopsipred -nojufo -samfile UapA_SAM.ss2 -id UapA_ UapA.fasta

        where UapA_SAM.ss2 is the SAM-predicted secondary structure in pripred_ss2 format, created in the following way: –sam UapA.rdb > UapA_SAM.ss2

        The UapA.rdb file has been obtained from ROBETTA server. Is this OK?

        The default weight file used for fragment picking by “” script is the following:
        # score name priority wght min_allowed extras
        ProfileScoreL1 700 1.0 –
        ProfileScoreStructL1 100 1.4 –
        SolventAccessibility 500 0.5 –
        Phi 300 3.9 –
        Psi 200 0.9 –

        No SecondarySimilarity and RamaScore are used. Are these priorities and weights suitable for picking fragments for membrane proteins? If not, could someone please recommend me some modifications?

        Thanks in advance,

      • #7180

          Isn’t there any membrane-guy reading this post?

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