{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T19:09:36Z","timestamp":1782241776524,"version":"3.54.5"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,9,22]],"date-time":"2023-09-22T00:00:00Z","timestamp":1695340800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2020YFA0712400"],"award-info":[{"award-number":["2020YFA0712400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11931008"],"award-info":[{"award-number":["11931008"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62272268"],"award-info":[{"award-number":["62272268"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Accurate identification of protein\u2013protein interaction (PPI) sites remains a computational challenge. We propose Spatom, a novel framework for PPI site prediction. This framework first defines a weighted digraph for a protein structure to precisely characterize the spatial contacts of residues, then performs a weighted digraph convolution to aggregate both spatial local and global information and finally adds an improved graph attention layer to drive the predicted sites to form more continuous region(s). Spatom was tested on a diverse set of challenging protein\u2013protein complexes and demonstrated the best performance among all the compared methods. Furthermore, when tested on multiple popular proteins in a case study, Spatom clearly identifies the interaction interfaces and captures the majority of hotspots. Spatom is expected to contribute to the understanding of protein interactions and drug designs targeting protein binding.<\/jats:p>","DOI":"10.1093\/bib\/bbad345","type":"journal-article","created":{"date-parts":[[2023,10,2]],"date-time":"2023-10-02T04:01:06Z","timestamp":1696219266000},"source":"Crossref","is-referenced-by-count":15,"title":["Spatom: a graph neural network for structure-based protein\u2013protein interaction site prediction"],"prefix":"10.1093","volume":"24","author":[{"given":"Haonan","family":"Wu","sequence":"first","affiliation":[{"name":"School of Mathematics and Statistics, Shandong University , Weihai 264209 , China"},{"name":"School of Mathematics, Shandong University , Jinan 250100 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiyun","family":"Han","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics, Shandong University , Weihai 264209 , 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