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I was wondering how one would find what part of a protein is bound by antibodies in the body. I would assume it's not the entire protein but a certain amino acid portion, or am I incorrect?

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It is indeed only a limited binding site, which is called an eptitope (and as a side note, while most common, antigens are not all proteins). There a range of options to identify epitopes, depending on what you start off with and what you want to figure out. They range from 3D analysis of high-resolution imaging of co-crystallized antigen-antibody complexes (which provides structural information but is costly and difficult and sometimes impossible to perform) to genetic methods. You will find more under the umbrella of epitope mapping.

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