Antibody Renumbering to AHo Scheme Unavailable on PyIgClassify Server

[yikzlim]

"According to RosettaAntibodyDesign (RAbD) manual: the input PDB file must be renumbered to the AHo Scheme. This can be done through the PyIgClassify Server (http://dunbrack2.fccc.edu/pyigclassify/)." However, it appears that the antibody renumbering feature is currently unavailable on the server interface. I am intending to renumber my antibody PDB file to AHo scheme for utilizing it as a starting structure for RosettaAntibodyDesign. If there are alternative recommendations or solutions to achieve AHo renumbering, I would appreciate your guidance.

[jadolfbr]

Hello, This has been down for some time now and I’m checking with my PhD lab if there is any way to get it up and running again. If this doesn’t work, I’ll make the pyigclassify2 code public (which we wanted to do anyway) and update the instructions. In the meantime, you Should be able to use ANARCI to renumber your antibody to Aho and although it has a few issues, it should work. Let me know how that goes - it is fairly easy to get going. It has a web server and a python tool you can install. https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabpred/anarci/

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-Jared

On Tue, Jan 14, 2025 at 10:44 PM yikzhenglim ***@***.***> wrote: "According to *RosettaAntibodyDesign (RAbD)* manual: the input PDB file must be renumbered to the *AHo Scheme*. This can be done through the *PyIgClassify* Server (http://dunbrack2.fccc.edu/pyigclassify/)." However, it appears that the antibody renumbering feature is currently unavailable on the server interface. I am intending to renumber my antibody PDB file to AHo scheme for utilizing it as a starting structure for RosettaAntibodyDesign. If there are alternative recommendations or solutions to achieve AHo renumbering, I would appreciate your guidance. — Reply to this email directly, view it on GitHub <#297>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZDHRAYCNAPA3JSHGXWVVD2KXKTBAVCNFSM6AAAAABVGJL2ECVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZXHAZDKNJTGA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[yikzlim]

Thank you for your reply. I’m really looking forward to the PyIgClassify2 code being made public.