{"entity": "publication", "iuid": "0013c1ea0aa54c31903307c143eca156", "timestamp": "2026-03-17T02:35:58.889Z", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0013c1ea0aa54c31903307c143eca156.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0013c1ea0aa54c31903307c143eca156"}}, "title": "ProQ3D: improved model quality assessments using deep learning.", "authors": [{"family": "Uziela", "given": "Karolis", "initials": "K"}, {"family": "Men\u00e9ndez Hurtado", "given": "David", "initials": "D"}, {"family": "Shu", "given": "Nanjiang", "initials": "N"}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2017-05-15", "journal": {"volume": "33", "issn": "1367-4811", "issue": "10", "pages": "1578-1580", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "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).\r\n\r\nProQ3D is freely available both as a webserver and a stand-alone program at http://proq3.bioinfo.se/.\r\n\r\narne@bioinfo.se.\r\n\r\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btw819", "pmid": "28052925", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "btw819"}], "notes": [], "created": "2017-11-01T12:35:54.198Z", "modified": "2020-01-21T13:53:21.650Z"}