{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T09:27:15Z","timestamp":1740130035202,"version":"3.37.3"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2021,5,8]],"date-time":"2021-05-08T00:00:00Z","timestamp":1620432000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Investissement d\u2019Avenir Infrastructures Nationales en Biologie et Sant\u00e9","award":["ANR-10-INBS-05-01","ANR-10-INBS-08","ANR-11-INBS-0013","ANR-18-IDEX-0001"],"award-info":[{"award-number":["ANR-10-INBS-05-01","ANR-10-INBS-08","ANR-11-INBS-0013","ANR-18-IDEX-0001"]}]},{"DOI":"10.13039\/501100001677","name":"Inserm","doi-asserted-by":"publisher","award":["U1133"],"award-info":[{"award-number":["U1133"]}],"id":[{"id":"10.13039\/501100001677","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Proteo3Dnet is a web server dedicated to the analysis of mass spectrometry interactomics experiments. Given a flat list of proteins, its aim is to organize it in terms of structural interactions to provide a clearer overview of the data. This is achieved using three means: (i) the search for interologs with resolved structure available in the protein data bank, including cross-species remote homology search, (ii) the search for possibly weaker interactions mediated through Short Linear Motifs as predicted by ELM\u2014a unique feature of Proteo3Dnet, (iii) the search for protein\u2013protein interactions physically validated in the BioGRID database. The server then compiles this information and returns a graph of the identified interactions and details about the different searches. The graph can be interactively explored to understand the way the core complexes identified could interact. It can also suggest undetected partners to the experimentalists, or specific cases of conditionally exclusive binding. The interest of Proteo3Dnet, previously demonstrated for the difficult cases of the proteasome and pragmin complexes data is, here, illustrated in the context of yeast precursors to the small ribosomal subunits and the smaller interactome of 14\u20133\u20133zeta frequent interactors. The Proteo3Dnet web server is accessible at http:\/\/bioserv.rpbs.univ-paris-diderot.fr\/services\/Proteo3Dnet\/.<\/jats:p>","DOI":"10.1093\/nar\/gkab332","type":"journal-article","created":{"date-parts":[[2021,4,19]],"date-time":"2021-04-19T22:31:51Z","timestamp":1618871511000},"page":"W567-W572","source":"Crossref","is-referenced-by-count":5,"title":["Proteo3Dnet: a web server for the integration of structural information with interactomics data"],"prefix":"10.1093","volume":"49","author":[{"given":"Guillaume","family":"Postic","sequence":"first","affiliation":[{"name":"Universit\u00e9 de Paris, CNRS UMR 8251, INSERM U1133, RPBS, Paris 75205, France"},{"name":"Institut Fran\u00e7ais de Bioinformatique (IFB), UMS 3601-CNRS, Universit\u00e9 Paris-Saclay, Orsay, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4435-9093","authenticated-orcid":false,"given":"Jessica","family":"Andreani","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198\u00a0Gif-sur-Yvette, France"}]},{"given":"Julien","family":"Marcoux","sequence":"additional","affiliation":[{"name":"Institut de Pharmacologie et de Biologie Structurale (IPBS), Universit\u00e9 de Toulouse, CNRS, UPS, Toulouse, France"}]},{"given":"Victor","family":"Reys","sequence":"additional","affiliation":[{"name":"Centre de Biochimie Structurale (CBS), CNRS, INSERM, Univ Montpellier, Montpellier, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5294-2858","authenticated-orcid":false,"given":"Rapha\u00ebl","family":"Guerois","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198\u00a0Gif-sur-Yvette, France"}]},{"given":"Julien","family":"Rey","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Paris, CNRS UMR 8251, INSERM U1133, RPBS, Paris 75205, France"}]},{"given":"Emmanuelle","family":"Mouton-Barbosa","sequence":"additional","affiliation":[{"name":"Institut de Pharmacologie et de Biologie Structurale (IPBS), Universit\u00e9 de Toulouse, CNRS, UPS, Toulouse, France"}]},{"given":"Yves","family":"Vandenbrouck","sequence":"additional","affiliation":[{"name":"Univ. Grenoble Alpes, INSERM, CEA, UMR BioSant\u00e9 U1292, CNRS, CEA, FR2048, 38000\u00a0Grenoble, France"}]},{"given":"Sarah","family":"Cianferani","sequence":"additional","affiliation":[{"name":"Laboratoire de Spectrom\u00e9trie de Masse BioOrganique, Universit\u00e9 de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France"}]},{"given":"Odile","family":"Burlet-Schiltz","sequence":"additional","affiliation":[{"name":"Institut de Pharmacologie et de Biologie Structurale (IPBS), Universit\u00e9 de Toulouse, CNRS, UPS, Toulouse, France"}]},{"given":"Gilles","family":"Labesse","sequence":"additional","affiliation":[{"name":"Centre de Biochimie Structurale (CBS), CNRS, INSERM, Univ Montpellier, Montpellier, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1033-9895","authenticated-orcid":false,"given":"Pierre","family":"Tuff\u00e9ry","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Paris, CNRS UMR 8251, INSERM U1133, RPBS, Paris 75205, France"}]}],"member":"286","published-online":{"date-parts":[[2021,5,8]]},"reference":[{"key":"2021070812053351900_B1","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1046\/j.1432-1033.2003.03428.x","article-title":"Affinity purification-mass spectrometry. powerful tools for the characterization of protein complexes","volume":"270","author":"Bauer","year":"2003","journal-title":"Eur. 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