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.
Hello,
I have asked the professor who has contributed to the PylgClassify. She told me that they have closed this function due to the security consideration. By the way, can you share some links for renumbering using ANARCI and the manual reworking from the ANARCI output to help us process the PDB files for RAbD! Thank you very much for your help!