{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/physical-epistatic-landscape-of-antibody","title":"Physical epistatic landscape of antibody binding affinity","arxiv_id":"1712.04000","date":"2017-12-11","proceeding":null,"authors":[],"abstract":"Affinity maturation produces antibodies that bind antigens with high\nspecificity by accumulating mutations in the antibody sequence. Mapping out the\nantibody-antigen affinity landscape can give us insight into the accessible\npaths during this rapid evolutionary process. By developing a carefully\ncontrolled null model for noninteracting mutations, we characterized epistasis\nin affinity measurements of a large library of antibody variants obtained by\nTite-Seq, a recently introduced Deep Mutational Scan method yielding physical\nvalues of the binding constant. We show that representing affinity as the\nbinding free energy minimizes epistasis. Yet, we find that epistatically\ninteracting sites contribute substantially to binding. In addition to negative\nepistasis, we report a large amount of beneficial epistasis, enlarging the\nspace of high-affinity antibodies as well as their mutational accessibility.\nThese properties suggest that the degeneracy of antibody sequences that can\nbind a given antigen is enhanced by epistasis - an important property for\nvaccine design.","url_abs":"http://arxiv.org/abs/1712.04000v1","url_pdf":"http://arxiv.org/pdf/1712.04000v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"physical-epistatic-landscape-of-antibody","repo_url":"https://github.com/rhys-m-adams/epistasis_4_4_20","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"specificity","task_name":"Specificity"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}