{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T02:09:43Z","timestamp":1773281383006,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2022,8,12]],"date-time":"2022-08-12T00:00:00Z","timestamp":1660262400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Shanghai Municipal Science and Technology Major Project","award":["2018SHZDZX01"],"award-info":[{"award-number":["2018SHZDZX01"]}]},{"name":"ZJLab"},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFF1200400"],"award-info":[{"award-number":["2021YFF1200400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Protein side chains are vitally important to many biological processes such as protein\u2013protein interaction. In this study, we evaluate the performance of our previous released side-chain modeling method OPUS-Mut, together with some other methods, on three oligomer datasets, CASP14 (11), CAMEO-Homo (65) and CAMEO-Hetero (21). The results show that OPUS-Mut outperforms other methods measured by all residues or by the interfacial residues. We also demonstrate our method on evaluating protein\u2013protein docking pose on a dataset Oligomer-Dock (75) created using the top 10 predictions from ZDOCK 3.0.2. Our scoring function correctly identifies the native pose as the top-1 in 45 out of 75 targets. Different from traditional scoring functions, our method is based on the overall side-chain packing favorableness in accordance with the local packing environment. It emphasizes the significance of side chains and provides a new and effective scoring term for studying protein\u2013protein interaction.<\/jats:p>","DOI":"10.1093\/bib\/bbac330","type":"journal-article","created":{"date-parts":[[2022,8,12]],"date-time":"2022-08-12T08:47:41Z","timestamp":1660294061000},"source":"Crossref","is-referenced-by-count":7,"title":["Studying protein\u2013protein interaction through side-chain modeling method OPUS-Mut"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0616-878X","authenticated-orcid":false,"given":"Gang","family":"Xu","sequence":"first","affiliation":[{"name":"Multiscale Research Institute of Complex Systems, Fudan University , Shanghai 200433 , China"},{"name":"Zhangjiang Fudan International Innovation Center, Fudan University , Shanghai 201210 , China"},{"name":"Shanghai AI Laboratory , Shanghai 200030 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yilin","family":"Wang","sequence":"additional","affiliation":[{"name":"Georgetown Preparatory School , North Bethesda, MD 20852 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qinghua","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Biomolecular Innovation, Harcam Biomedicines , Shanghai , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianpeng","family":"Ma","sequence":"additional","affiliation":[{"name":"Multiscale Research Institute of Complex Systems, Fudan University , Shanghai 200433 , China"},{"name":"Zhangjiang Fudan International Innovation Center, Fudan University , Shanghai 201210 , China"},{"name":"Shanghai AI Laboratory , Shanghai 200030 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,8,12]]},"reference":[{"key":"2022092013232956700_ref1","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1109\/TCBB.2019.2953908","article-title":"Imbalance data processing strategy for protein interaction sites prediction","volume":"18","author":"Wang","year":"2021","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"2022092013232956700_ref2","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1093\/bib\/bbv027","article-title":"Progress and challenges in predicting protein interfaces","volume":"17","author":"Esmaielbeiki","year":"2016","journal-title":"Brief Bioinform"},{"key":"2022092013232956700_ref3","doi-asserted-by":"crossref","first-page":"1328","DOI":"10.1110\/ps.041222905","article-title":"Improved side-chain modeling for protein-protein docking","volume":"14","author":"Wang","year":"2005","journal-title":"Protein 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