{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,9]],"date-time":"2026-05-09T15:18:54Z","timestamp":1778339934483,"version":"3.51.4"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,3]],"date-time":"2025-01-03T00:00:00Z","timestamp":1735862400000},"content-version":"vor","delay-in-days":42,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100018625","name":"Science and Technology Innovation Plan Of Shanghai Science and Technology Commission","doi-asserted-by":"publisher","award":["23S41900400"],"award-info":[{"award-number":["23S41900400"]}],"id":[{"id":"10.13039\/501100018625","id-type":"DOI","asserted-by":"publisher"}]},{"name":"AI for Science Foundation of Fudan University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Proteins can be represented in different data forms, including sequence, structure, and surface, each of which has unique advantages and certain limitations. It is promising to fuse the complementary information among them. In this work, we propose a framework called ProteinF3S for enzyme function prediction that fuses the complementary information across protein sequence, structure, and surface. To achieve more effective fusion, we propose a multi-scale bidirectional fusion strategy between protein structure and surface, in which the hierarchical features of a surface encoder and a structure encoder interact with each other bidirectionally. Based on these interactions, more distinctive features can be obtained. After that, we achieve further fusion by concatenating the sequence features with the features containing structure and surface information, so that better performance can be achieved. To validate our method, we conduct extensive experiments on tasks including enzyme reaction classification and enzyme commission number prediction. Our method achieves new state-of-the-art performance and shows that fusing different forms of data is effective in enzyme function prediction.<\/jats:p>","DOI":"10.1093\/bib\/bbae695","type":"journal-article","created":{"date-parts":[[2025,1,3]],"date-time":"2025-01-03T13:21:42Z","timestamp":1735910502000},"source":"Crossref","is-referenced-by-count":5,"title":["ProteinF3S: boosting enzyme function prediction by fusing protein sequence, structure, and surface"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1322-7530","authenticated-orcid":false,"given":"Mingzhi","family":"Yuan","sequence":"first","affiliation":[{"name":"Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","place":["China"]},{"name":"Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","place":["China"]},{"name":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-1937-6855","authenticated-orcid":false,"given":"Ao","family":"Shen","sequence":"additional","affiliation":[{"name":"Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","place":["China"]},{"name":"Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","place":["China"]},{"name":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-7335-785X","authenticated-orcid":false,"given":"Yingfan","family":"Ma","sequence":"additional","affiliation":[{"name":"Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","place":["China"]},{"name":"Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","place":["China"]},{"name":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Du","sequence":"additional","affiliation":[{"name":"Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","place":["China"]},{"name":"Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","place":["China"]},{"name":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai 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