VH-VL Orientation in antibody

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    • June 17, 2019 at 8:23 am #3180
      Anonymous

         

        How to determine the VH-VL orientation angle in rosetta. i came across this manuscript “Improved prediction of antibody VL–VH orientation” by Protein Eng Des Sel. 2016 Oct; 29(10): 409–418. Here there is description of MT protocol. Whether the script is provided in the rosetta 3.1 version. Or is there any other alternative in rosetta to calculate the VH-VL orientation (LHOC) angle of antibody in rosetta.

        Antcipating a reply soon

        Thanking you

        Dr. Suji george

        Scientist C

        National Institute of Virology

        pune, Maharashtra, INDIA.

      • June 17, 2019 at 1:03 pm #14778
        Anonymous

          Dr. Suji,

          I am not 100% certain when the application was moved to be public, but in the newer versions of Rosetta (3.7 and newer), you can run the “packing_angle” application to calculate the four metrics, then the LHOC is just the z-score of those metrics relative to the means/std. devs. described in the paper you are referencing. 

          See also https://www.rosettacommons.org/docs/latest/Release-Notes for more information on which tools is available when.

          Best,

          Jeliazko

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