Hi everyone
I want to model antibody structure but I do not have the sequence of the whole antibody. I just have the sequence of its CDR region. Do you know any web server to model antibody structure by grafting CDR regions on the structure of the antibody?
Take the sequences of an antibody containing the framework combination you wish to use, e.g. human Vkappa1/human VH3 consensus for a well-folding and stable framework,
(DIQMTQSPSSLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRT, EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARWGGDGFYAMDYWGQGTLVTVSS). If you know the germline family of your antibody, but not the exact framework sequence, you can also substitute the closest germline sequences
Replace the original CDR sequences in this antibody sequences with your own CDR sequences (see https://plueckthun.bioc.uzh.ch/antibody/Numbering/SeqHeader.html , https://plueckthun.bioc.uzh.ch/antibody/Numbering/Numbering.html for a comparison of different CDR definitions to match the one corresponding to the sequences you have).
You can then submit the resulting sequences to an antibody modelling server, e.g. https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabpred/ to generate a 3D model
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