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.
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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