{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T14:18:27Z","timestamp":1774448307459,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,12,2]],"date-time":"2021-12-02T00:00:00Z","timestamp":1638403200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Cancer Institute, National Institutes of Health","award":["HHSN26120080001E"],"award-info":[{"award-number":["HHSN26120080001E"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We present a web-based server for navigating and visualizing possible interactions between SARS-CoV-2 and human host proteins. The interactions are obtained from HMI_Pred which relies on the rationale that virus proteins mimic host proteins. The structural alignment of the viral protein with one side of the human protein\u2013protein interface determines the mimicry. The mimicked human proteins and predicted interactions, and the binding sites are presented. The user can choose one of the 18 SARS-CoV-2 protein structures and visualize the potential 3D complexes it forms with human proteins. The mimicked interface is also provided. The user can superimpose two interacting human proteins in order to see whether they bind to the same site or different sites on the viral protein. The server also tabulates all available mimicked interactions together with their match scores and number of aligned residues. This is the first server listing and cataloging all interactions between SARS-CoV-2 and human protein structures, enabled by our innovative interface mimicry strategy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The server is available at https:\/\/interactome.ku.edu.tr\/sars\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab799","type":"journal-article","created":{"date-parts":[[2021,11,25]],"date-time":"2021-11-25T20:17:58Z","timestamp":1637871478000},"page":"1455-1457","source":"Crossref","is-referenced-by-count":5,"title":["SARS-CoV-2 Interactome 3D: A Web interface for 3D visualization and analysis of SARS-CoV-2\u2013human mimicry and interactions"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5300-8098","authenticated-orcid":false,"given":"Damla","family":"Ovek","sequence":"first","affiliation":[{"name":"Department of Computer Engineering, Koc University , Bank AI Center, Istanbul 34450, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ameer","family":"Taweel","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, Koc University , Bank AI Center, Istanbul 34450, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zeynep","family":"Abali","sequence":"additional","affiliation":[{"name":"Graduate School of Science and Engineering, Koc University , Bank AI Center, Istanbul 24450, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ece","family":"Tezsezen","sequence":"additional","affiliation":[{"name":"Graduate School of Science and Engineering, Koc University , Bank AI Center, Istanbul 24450, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1471-7294","authenticated-orcid":false,"given":"Yunus Emre","family":"Koroglu","sequence":"additional","affiliation":[{"name":"Graduate School of Science and Engineering, Koc University , Bank AI Center, Istanbul 24450, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chung-Jung","family":"Tsai","sequence":"additional","affiliation":[{"name":"Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick , Frederick, MD 21702, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruth","family":"Nussinov","sequence":"additional","affiliation":[{"name":"Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick , Frederick, MD 21702, USA"},{"name":"Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University , Tel Aviv 69978, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ozlem","family":"Keskin","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biological Engineering, Koc University , Istanbul 34450, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2297-2113","authenticated-orcid":false,"given":"Attila","family":"Gursoy","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, Koc University , Bank AI Center, Istanbul 34450, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,12,2]]},"reference":[{"key":"2023020108542866400_btab799-B1","doi-asserted-by":"crossref","first-page":"W285","DOI":"10.1093\/nar\/gku397","article-title":"PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes","volume":"42","author":"Baspinar","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020108542866400_btab799-B2","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1080\/21505594.2020.1726594","article-title":"Orchestrated efforts on host network hijacking: processes governing virus replication","volume":"11","author":"Dai","year":"2020","journal-title":"Virulence"},{"key":"2023020108542866400_btab799-B3","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1038\/s41586-020-2286-9","article-title":"A SARS-CoV-2 protein interaction map reveals targets for drug repurposing","volume":"583","author":"Gordon","year":"2020","journal-title":"Nature"},{"key":"2023020108542866400_btab799-B4","doi-asserted-by":"crossref","first-page":"3925","DOI":"10.1016\/j.jmb.2017.10.023","article-title":"Prediction of host-pathogen interactions for helicobacter pylori by interface mimicry and implications to gastric cancer","volume":"429","author":"Guven-Maiorov","year":"2017","journal-title":"J. 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