{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T15:46:19Z","timestamp":1784303179943,"version":"3.55.0"},"reference-count":107,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,3,5]],"date-time":"2021-03-05T00:00:00Z","timestamp":1614902400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61602352"],"award-info":[{"award-number":["61602352"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Pioneer Hundred Talents Program of Chinese Academy of Sciences and the NSFC Excellent Young Scholars Program","award":["61722212"],"award-info":[{"award-number":["61722212"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Proteins interact with each other to play critical roles in many biological processes in cells. Although promising, laboratory experiments usually suffer from the disadvantages of being time-consuming and labor-intensive. The results obtained are often not robust and considerably uncertain. Due recently to advances in high-throughput technologies, a large amount of proteomics data has been collected and this presents a significant opportunity and also a challenge to develop computational models to predict protein\u2013protein interactions (PPIs) based on these data. In this paper, we present a comprehensive survey of the recent efforts that have been made towards the development of effective computational models for PPI prediction. The survey introduces the algorithms that can be used to learn computational models for predicting PPIs, and it classifies these models into different categories. To understand their relative merits, the paper discusses different validation schemes and metrics to evaluate the prediction performance. Biological databases that are commonly used in different experiments for performance comparison are also described and their use in a series of extensive experiments to compare different prediction models are discussed. Finally, we present some open issues in PPI prediction for future work. We explain how the performance of PPI prediction can be improved if these issues are effectively tackled.<\/jats:p>","DOI":"10.1093\/bib\/bbab036","type":"journal-article","created":{"date-parts":[[2021,2,28]],"date-time":"2021-02-28T12:09:19Z","timestamp":1614514159000},"source":"Crossref","is-referenced-by-count":168,"title":["A survey on computational models for predicting protein\u2013protein interactions"],"prefix":"10.1093","volume":"22","author":[{"given":"Lun","family":"Hu","sequence":"first","affiliation":[{"name":"Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 830011, Urumqi, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaojuan","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Wuhan University of Technology, 430070, Wuhan, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-An","family":"Huang","sequence":"additional","affiliation":[{"name":"College of Computer Science and Software Engineering, Shenzhen University, 518060, Shenzhen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengwei","family":"Hu","sequence":"additional","affiliation":[{"name":"IBM Research, 100193, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhu-Hong","family":"You","sequence":"additional","affiliation":[{"name":"Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 830011, Urumqi, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,3,5]]},"reference":[{"key":"2021090815135368300_ref1","first-page":"D408","article-title":"Hippie v2. 0: enhancing meaningfulness and reliability of protein\u2013protein interaction networks","volume-title":"Nucleic Acids Res","author":"Alanis-Lobato","year":"2016"},{"issue":"suppl_1","key":"2021090815135368300_ref2","doi-asserted-by":"crossref","first-page":"D226","DOI":"10.1093\/nar\/gkh039","article-title":"Scop database in 2004: refinements integrate structure and sequence family data","volume":"32","author":"Andreeva","year":"2004","journal-title":"Nucleic Acids Res"},{"issue":"4096","key":"2021090815135368300_ref3","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1126\/science.181.4096.223","article-title":"Principles that govern the folding of protein chains","volume":"181","author":"Anfinsen","year":"1973","journal-title":"Science"},{"issue":"1","key":"2021090815135368300_ref4","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1093\/nar\/gkg056","article-title":"Christopher WV Hogue. 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