{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T00:36:34Z","timestamp":1781224594416,"version":"3.54.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T00:00:00Z","timestamp":1683936000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-2145226"],"award-info":[{"award-number":["DBI-2145226"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Predicting protein localization and understanding its mechanisms are critical in biology and pathology. In this context, we propose a new web application of MULocDeep with improved performance, result interpretation, and visualization. By transferring the original model into species-specific models, MULocDeep achieved competitive prediction performance at the subcellular level against other state-of-the-art methods. It uniquely provides a comprehensive localization prediction at the suborganellar level. Besides prediction, our web service quantifies the contribution of single amino acids to localization for individual proteins; for a group of proteins, common motifs or potential targeting-related regions can be derived. Furthermore, the visualizations of targeting mechanism analyses can be downloaded for publication-ready figures. The MULocDeep web service is available at https:\/\/www.mu-loc.org\/.<\/jats:p>","DOI":"10.1093\/nar\/gkad374","type":"journal-article","created":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T10:23:15Z","timestamp":1683973395000},"page":"W343-W349","source":"Crossref","is-referenced-by-count":44,"title":["MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels"],"prefix":"10.1093","volume":"51","author":[{"given":"Yuexu","family":"Jiang","sequence":"first","affiliation":[{"name":"Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri , Columbia , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri , Columbia , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chopparapu Sai","family":"Akhil","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri , Columbia , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Duolin","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri , Columbia , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziyang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri , Columbia , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weinan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri , Columbia , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4809-0514","authenticated-orcid":false,"given":"Dong","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri , Columbia , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,13]]},"reference":[{"key":"2023070504573035900_B1","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1038\/nrd2897","article-title":"Subcellular targeting strategies for drug design and delivery","volume":"9","author":"Rajendran","year":"2010","journal-title":"Nat. Rev. Drug Discov."},{"key":"2023070504573035900_B2","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1007\/s11095-006-9133-z","article-title":"Controlling protein compartmentalization to overcome disease","volume":"24","author":"Davis","year":"2006","journal-title":"Pharm. Res."},{"key":"2023070504573035900_B3","doi-asserted-by":"crossref","first-page":"3381","DOI":"10.1242\/jcs.089110","article-title":"Protein localization in disease and therapy","volume":"124","author":"Hung","year":"2011","journal-title":"J. Cell Sci."},{"key":"2023070504573035900_B4","doi-asserted-by":"crossref","first-page":"26947","DOI":"10.1074\/jbc.M101870200","article-title":"Multiple mechanisms regulate subcellular localization of human CDC6","volume":"276","author":"Delmolino","year":"2001","journal-title":"J. Biol. Chem."},{"key":"2023070504573035900_B5","doi-asserted-by":"crossref","first-page":"13","DOI":"10.3389\/fcell.2018.00013","article-title":"Subcellular localization and dynamics of the Bcl-2 family of proteins","volume":"6","author":"Popgeorgiev","year":"2018","journal-title":"Front. Cell Dev. Biol."},{"key":"2023070504573035900_B6","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1126\/science.286.5440.666","article-title":"Protein ZIP codes make nobel journey","volume":"286","author":"Hagmann","year":"1999","journal-title":"Science"},{"key":"2023070504573035900_B7","article-title":"ProtTrans: towards cracking the language of lifes code through self-supervised deep learning and high performance computing","author":"Elnaggar","year":"2021","journal-title":"IEEE Trans. Pattern Anal. Mach. Intell."},{"key":"2023070504573035900_B8","doi-asserted-by":"crossref","first-page":"vbab035","DOI":"10.1093\/bioadv\/vbab035","article-title":"Light attention predicts protein location from the language of life","volume":"1","author":"St\u00e4rk","year":"2021","journal-title":"Bioinform. Adv."},{"key":"2023070504573035900_B9","doi-asserted-by":"crossref","first-page":"3387","DOI":"10.1093\/bioinformatics\/btx431","article-title":"DeepLoc: prediction of protein subcellular localization using deep learning","volume":"33","author":"Almagro\u00a0Armenteros","year":"2017","journal-title":"Bioinformatics"},{"key":"2023070504573035900_B10","doi-asserted-by":"crossref","first-page":"W228","DOI":"10.1093\/nar\/gkac278","article-title":"DeepLoc 2.0: multi-label subcellular localization prediction using protein language models","volume":"50","author":"Thumuluri","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023070504573035900_B11","doi-asserted-by":"crossref","first-page":"4825","DOI":"10.1016\/j.csbj.2021.08.027","article-title":"MULocDeep: a deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation","volume":"19","author":"Jiang","year":"2021","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"2023070504573035900_B12","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1093\/bioinformatics\/btz512","article-title":"DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks","volume":"36","author":"Savojardo","year":"2020","journal-title":"Bioinformatics"},{"key":"2023070504573035900_B13","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1093\/bioinformatics\/btw656","article-title":"SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments","volume":"33","author":"Savojardo","year":"2016","journal-title":"Bioinformatics"},{"key":"2023070504573035900_B14","doi-asserted-by":"crossref","first-page":"e98345","DOI":"10.1371\/journal.pone.0098345","article-title":"Protein Sub-Nuclear Localization Prediction Using SVM and Pfam Domain Information","volume":"9","author":"Kumar","year":"2014","journal-title":"PLoS One"},{"key":"2023070504573035900_B15","doi-asserted-by":"crossref","first-page":"e201900429","DOI":"10.26508\/lsa.201900429","article-title":"Detecting sequence signals in targeting peptides using deep learning","volume":"2","author":"Almagro\u00a0Armenteros","year":"2019","journal-title":"Life Sci. Alliance"},{"key":"2023070504573035900_B16","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1038\/s41587-021-01156-3","article-title":"SignalP 6.0 predicts all five types of signal peptides using protein language models","volume":"40","author":"Teufel","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"2023070504573035900_B17","doi-asserted-by":"crossref","first-page":"5834","DOI":"10.1016\/j.csbj.2021.10.023","article-title":"Computational methods for protein localization prediction","volume":"19","author":"Jiang","year":"2021","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"2023070504573035900_B18","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1162\/neco.1997.9.8.1735","article-title":"Long short-term memory","volume":"9","author":"Hochreiter","year":"1997","journal-title":"Neural Comput."},{"key":"2023070504573035900_B19","article-title":"A structured self-attentive sentence embedding","author":"Lin","year":"2017"},{"key":"2023070504573035900_B20","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1016\/0968-0004(91)90184-W","article-title":"Nuclear targeting sequences \u2014 a consensus?","volume":"16","author":"Dingwall","year":"1991","journal-title":"Trends Biochem. Sci"},{"key":"2023070504573035900_B21","first-page":"241","article-title":"Changes in biliary secretory immunoglobulins A in mice fed whey proteins]","volume":"35","author":"Costantino","year":"1989","journal-title":"Minerva Dietol. Gastroenterol."},{"key":"2023070504573035900_B22","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/0378-1119(90)90281-U","article-title":"Novel use of a chimpanzee pseudogene for chromosomal mapping of human cytochrome oxidase subunitIV","volume":"86","author":"Lomax","year":"1990","journal-title":"Gene"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W343\/50736443\/gkad374.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W343\/50736443\/gkad374.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T09:25:01Z","timestamp":1688549101000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/W1\/W343\/7161528"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5,13]]},"references-count":22,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2023,5,13]]},"published-print":{"date-parts":[[2023,7,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkad374","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,7,5]]},"published":{"date-parts":[[2023,5,13]]}}}