Hi,
I've been trying to use the Anibody Designer but i was unable to use PyIgClassify webserver to renumber and label the CDRs in my PDB file. I am also unable to get it to find CDRs in any antibody pdb file even thoughs its within the database. I would also like to find the schema for how the CDRs are marked within the text of the renumbered PDB file. Any help would be appreciated.
Thanks,
Will
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Hello,
Have you tried PyIgClassify2? If this does not work, I would recommend renumbering using ANARCI. You may need to do some manual reworking from the ANARCI output, but the renumbering can be AHO which RAbD will use.
Does the original PyIgClassify give an error?
The CDRs are found after renumbering. Renumbering is done after HMMER using different HMMs for the different chains. Similar to alignments. The paper does cover this a bit if you want to read a bit more.