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In this article, we present various methods for representing protein 3D structures from low- to high-resolution, and show how interpretable ML methods can support tasks such as predicting protein structures, protein functions, and protein-protein interactions. This survey also emphasizes the significance of interpreting and visualizing ML-based inference for structure-based protein representations that enhance interpretability and knowledge discovery. Developing such interpretable approaches promises to further accelerate fields, including drug development and protein design.<\/jats:p>","DOI":"10.1145\/3801737","type":"journal-article","created":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T21:00:57Z","timestamp":1773867657000},"page":"1-24","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Interpretable Machine Learning for Protein Science: Structure, Function, and Interactions"],"prefix":"10.1145","volume":"58","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2862-6200","authenticated-orcid":false,"given":"Luiz Felipe","family":"Vecchietti","sequence":"first","affiliation":[{"name":"Max Planck Institute for Security and Privacy","place":["Bochum, Germany"]},{"name":"Institute for Basic Science","place":["Bochum, Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5293-8904","authenticated-orcid":false,"given":"Minji","family":"Lee","sequence":"additional","affiliation":[{"name":"Columbia University","place":["New York, USA"]},{"name":"Korea Advanced Institute of Science and Technology","place":["New York, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-2614-8843","authenticated-orcid":false,"given":"Begench","family":"Hangeldiyev","sequence":"additional","affiliation":[{"name":"Korea Advanced Institute of Science and Technology","place":["Daejeon, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-3509-0519","authenticated-orcid":false,"given":"Bryan Nathanael","family":"Wijaya","sequence":"additional","affiliation":[{"name":"Korea Advanced Institute of Science and Technology","place":["Daejeon, Republic of Korea"]},{"name":"Max Planck Institute for Security and Privacy","place":["Daejeon, Republic of Korea"]},{"name":"Institute for Basic Science","place":["Daejeon, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-3725-4092","authenticated-orcid":false,"given":"Hyunkyu","family":"Jung","sequence":"additional","affiliation":[{"name":"Korea Advanced Institute of Science and Technology","place":["Daejeon, Republic of Korea"]},{"name":"Institute for Basic Science","place":["Daejeon, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7129-1912","authenticated-orcid":false,"given":"Hahnbeom","family":"Park","sequence":"additional","affiliation":[{"name":"Korea Institute of Science and Technology","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7587-6053","authenticated-orcid":false,"given":"Tae-Kyun","family":"Kim","sequence":"additional","affiliation":[{"name":"Korea Advanced Institute of Science and Technology","place":["Daejeon, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4085-9648","authenticated-orcid":false,"given":"Meeyoung","family":"Cha","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Security and Privacy","place":["Bochum, Germany"]},{"name":"Korea Advanced Institute of Science and Technology","place":["Bochum, Germany"]},{"name":"Institute for Basic Science","place":["Bochum, Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0029-3643","authenticated-orcid":false,"given":"Ho Min","family":"Kim","sequence":"additional","affiliation":[{"name":"Korea Advanced Institute of Science and Technology","place":["Daejeon, Republic of Korea"]},{"name":"Institute for Basic Science","place":["Daejeon, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"320","published-online":{"date-parts":[[2026,4,25]]},"reference":[{"key":"e_1_3_1_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07487-w"},{"key":"e_1_3_1_3_2","doi-asserted-by":"crossref","unstructured":"Etowah Adams Liam Bai Minji Lee Yiyang Yu and Mohammed Alquraishi. 2025. 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