{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T19:53:35Z","timestamp":1792094015583,"version":"4.4.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2017,1,4]],"date-time":"2017-01-04T00:00:00Z","timestamp":1483488000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"crossref","award":["VR-NT 2012-5046"],"award-info":[{"award-number":["VR-NT 2012-5046"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"crossref","award":["2012-5270"],"award-info":[{"award-number":["2012-5270"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100017156","name":"Swedish e-Science Research Center","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100017156","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Swedish National Infrastructure for Computing"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Protein quality assessment is a long-standing problem in bioinformatics. For more than a decade we have developed state-of-art predictors by carefully selecting and optimising inputs to a machine learning method. The correlation has increased from 0.60 in ProQ to 0.81 in ProQ2 and 0.85 in ProQ3 mainly by adding a large set of carefully tuned descriptions of a protein. Here, we show that a substantial improvement can be obtained using exactly the same inputs as in ProQ2 or ProQ3 but replacing the support vector machine by a deep neural network. This improves the Pearson correlation to 0.90 (0.85 using ProQ2 input features).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>ProQ3D is freely available both as a webserver and a stand-alone program at http:\/\/proq3.bioinfo.se\/<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw819","type":"journal-article","created":{"date-parts":[[2016,12,20]],"date-time":"2016-12-20T12:05:51Z","timestamp":1482235551000},"page":"1578-1580","source":"Crossref","is-referenced-by-count":175,"title":["ProQ3D: improved model quality assessments using deep learning"],"prefix":"10.1093","volume":"33","author":[{"given":"Karolis","family":"Uziela","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Men\u00e9ndez Hurtado","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nanjiang","family":"Shu","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden"},{"name":"Bioinformatics Short-term Support and Infrastructure (BILS), Science for Life Laboratory, Solna, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bj\u00f6rn","family":"Wallner","sequence":"additional","affiliation":[{"name":"Department of Physics, Chemistry and Biology (IFM)\/Bioinformatics. Link\u00f6ping University, \u2009Link\u00f6ping, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arne","family":"Elofsson","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,1,4]]},"reference":[{"key":"2023020205102452000_btw819-B1","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1002\/prot.21715","article-title":"QMEAN: A comprehensive scoring function for model quality assessment","volume":"71","author":"Benkert","year":"2008","journal-title":"Proteins"},{"key":"2023020205102452000_btw819-B2","doi-asserted-by":"crossref","first-page":"23990.","DOI":"10.1038\/srep23990","article-title":"Protein single-model quality assessment by feature-based probability density functions","volume":"6","author":"Cao","year":"2016","journal-title":"Sci. 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