membrane protein packing prediction

Member Site Forums Rosetta 3 Rosetta 3 – General membrane protein packing prediction

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    • #1137

        Hi, fellows:
        We have two transmembrane peptide from two separate membrane proteins and we would like to see how they pack. The conformation of helix 1, i.e., tilt angle w.r.t the membrane etc, is determined by NMR. For the second helix, we currently take it as an ideal helix. The tilt angle for helix 2 is also known. This problem is similar to the glycophorin A packing problem addressed in “Toward high-resolution prediction and design of transmembrane helical protein structures”.
        Does anyone know how to use membrane_abinitio or docking_protocl+score_membrane to predict the packing conformation of these two helices?
        Thank you.

      • #6563

          I know Patrick answered this via email – did it work out…?

        • #6616

            Hi smlewis,

            I also have a similar problem with membrane docking. Would you like to paste the method Patrick provided in his email.

            Thanks a lot!
            -Justin Zhang

          • #6617

              I never got it – I’ve requested someone send it along so I can archive it here.

            • #6959

                Yes, this is interesting to many of us.
                Posting a solution here would be great.
                best wishes…

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