{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,25]],"date-time":"2026-05-25T15:04:30Z","timestamp":1779721470664,"version":"3.53.1"},"reference-count":71,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,5,25]],"date-time":"2026-05-25T00:00:00Z","timestamp":1779667200000},"content-version":"vor","delay-in-days":24,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32270689"],"award-info":[{"award-number":["32270689"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Understanding protein functions in biological processes is pivotal for disease elucidation and drug discovery. Despite notable progress, existing approaches primarily focus on function transfer under in-distribution (ID) settings, where training and test proteins exhibit high sequence similarity. As a result, their performance often degrades when applied to novel, diverse, and low-homology protein sequences, posing a major challenge for out-of-distribution (OOD) generalization encountered in practice. Towards this end, we develop ProteinScore, a graph transformer approach tailored to improve protein function prediction in OOD settings. ProteinScore integrates a label-invariant variational subgraph generator with self-supervised contrastive learning, thereby identifying meaning substructures within proteins. By highlighting informative features while filtering out redundant ones, ProteinScore improves generalization to diverse and low-homology sequences. Experiments on datasets with both experimentally resolved and AlphaFold2-predicted structures demonstrate that ProteinScore consistently outperforms strong baselines and provides biologically meaningful interpretability through accurately identifying binding sites. In addition, ProteinScore generalizes effectively to two additional downstream tasks, drug\u2013target interaction classification and subcellular localization prediction, achieving superior predictive performance and reliable interpretability.<\/jats:p>","DOI":"10.1093\/bib\/bbag243","type":"journal-article","created":{"date-parts":[[2026,5,25]],"date-time":"2026-05-25T14:36:51Z","timestamp":1779719811000},"source":"Crossref","is-referenced-by-count":0,"title":["Out-of-distribution generalization enhances protein function annotation for low-homology sequences"],"prefix":"10.1093","volume":"27","author":[{"given":"Yiwei","family":"Fu","sequence":"first","affiliation":[{"name":"School of Mathematical Sciences, Peking University , No. 5, Yiheyuan Road, Haidian District, Beijing 100871,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaxiao","family":"Chen","sequence":"additional","affiliation":[{"name":"Center for Quantitative Biology, Peking University , No. 5, Yiheyuan Road, Haidian District, Beijing 100871,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haoyu","family":"Lin","sequence":"additional","affiliation":[{"name":"Center for Quantitative Biology, Peking University , No. 5, Yiheyuan Road, Haidian District, Beijing 100871,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhonghui","family":"Gu","sequence":"additional","affiliation":[{"name":"Peking-Tsinghua Center for Life Sciences, Peking University , No. 5, Yiheyuan Road, Haidian District, Beijing 100871,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingqing","family":"Long","sequence":"additional","affiliation":[{"name":"School of Computer Science, Peking University , No. 5, Yiheyuan Road, Haidian District, Beijing 100871,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Wan","sequence":"additional","affiliation":[{"name":"School of Mathematical Sciences, Peking University , No. 5, Yiheyuan Road, Haidian District, Beijing 100871,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao","family":"Luo","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Wisconsin\u2013Madison , 1205 University Avenue, Madison, WI 53706,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minghua","family":"Deng","sequence":"additional","affiliation":[{"name":"School of Mathematical Sciences, Peking University , No. 5, Yiheyuan Road, Haidian District, Beijing 100871,","place":["China"]},{"name":"Center for Quantitative Biology, Peking University , No. 5, Yiheyuan Road, Haidian District, Beijing 100871,","place":["China"]},{"name":"Center for Statistical Science, Peking 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