Thanks for sharing this interesting approach to model antigen and antibody interaction.
I am trying to evalutate the model quality based on the server that you published http://www.zzdlab.com/AbAgIntPre/ but wondering how to correctly use it.
Could you explain how do you define the fv region? What residues are you considering? Do you simply extract certain regions e.g.
CDR1 27 <= resseq <= 38,
CDR2 56 <= resseq <= 65,
CDR3 105 <= resseq <= 117, or do you use a tool to determine the fv region?
Do you use the complete antigen sequence or only use the epitope, if yes how do you extract the epitope?
Thanks for sharing this interesting approach to model antigen and antibody interaction. I am trying to evalutate the model quality based on the server that you published http://www.zzdlab.com/AbAgIntPre/ but wondering how to correctly use it. Could you explain how do you define the fv region? What residues are you considering? Do you simply extract certain regions e.g. CDR1 27 <= resseq <= 38, CDR2 56 <= resseq <= 65, CDR3 105 <= resseq <= 117, or do you use a tool to determine the fv region? Do you use the complete antigen sequence or only use the epitope, if yes how do you extract the epitope?