{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T02:10:11Z","timestamp":1773281411935,"version":"3.50.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,9,3]],"date-time":"2021-09-03T00:00:00Z","timestamp":1630627200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Shanghai Municipal Science and Technology Major Project","award":["2018SHZDZX01"],"award-info":[{"award-number":["2018SHZDZX01"]}]},{"DOI":"10.13039\/100000928","name":"Welch Foundation","doi-asserted-by":"publisher","award":["Q-1826"],"award-info":[{"award-number":["Q-1826"]}],"id":[{"id":"10.13039\/100000928","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000928","name":"Welch Foundation","doi-asserted-by":"publisher","award":["Q-1512"],"award-info":[{"award-number":["Q-1512"]}],"id":[{"id":"10.13039\/100000928","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The development of an open-source platform to predict protein 1D features and 3D structure is an important task. In this paper, we report an open-source toolkit for protein 3D structure modeling, named OPUS-X. It contains three modules: OPUS-TASS2, which predicts protein torsion angles, secondary structure and solvent accessibility; OPUS-Contact, which measures the distance and orientation information between different residue pairs; and OPUS-Fold2, which uses the constraints derived from the first two modules to guide folding.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>OPUS-TASS2 is an upgraded version of our previous method OPUS-TASS. OPUS-TASS2 integrates protein global structure information and significantly outperforms OPUS-TASS. OPUS-Contact combines multiple raw co-evolutionary features with protein 1D features predicted by OPUS-TASS2, and delivers better results than the open-source state-of-the-art method trRosetta. OPUS-Fold2 is a complementary version of our previous method OPUS-Fold. OPUS-Fold2 is a gradient-based protein folding framework based on the differentiable energy terms in opposed to OPUS-Fold that is a sampling-based method used to deal with the non-differentiable terms. OPUS-Fold2 exhibits comparable performance to the Rosetta folding protocol in trRosetta when using identical inputs. OPUS-Fold2 is written in Python and TensorFlow2.4, which is user-friendly to any source-code-level modification.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availabilityand implementation<\/jats:title>\n                    <jats:p>The code and pre-trained models of OPUS-X can be downloaded from https:\/\/github.com\/OPUS-MaLab\/opus_x.<\/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\/btab633","type":"journal-article","created":{"date-parts":[[2021,9,3]],"date-time":"2021-09-03T13:07:59Z","timestamp":1630674479000},"page":"108-114","source":"Crossref","is-referenced-by-count":7,"title":["OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding"],"prefix":"10.1093","volume":"38","author":[{"given":"Gang","family":"Xu","sequence":"first","affiliation":[{"name":"Multiscale Research Institute of Complex Systems, Fudan University , Shanghai 200433, China"},{"name":"Zhangjiang Fudan International Innovation Center, Fudan University , Shanghai 201210, China"},{"name":"Shanghai AI Laboratory , Shanghai 200030, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qinghua","family":"Wang","sequence":"additional","affiliation":[{"name":"Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2943-0779","authenticated-orcid":false,"given":"Jianpeng","family":"Ma","sequence":"additional","affiliation":[{"name":"Multiscale Research Institute of Complex Systems, Fudan University , Shanghai 200433, China"},{"name":"Zhangjiang Fudan International Innovation Center, Fudan University , Shanghai 201210, China"},{"name":"Shanghai AI Laboratory , Shanghai 200030, China"},{"name":"Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,9,3]]},"reference":[{"key":"2023020108400905900_btab633-B1","first-page":"265","author":"Abadi","year":"2016"},{"key":"2023020108400905900_btab633-B2","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023020108400905900_btab633-B3","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1107\/S0907444998003254","article-title":"Crystallography & NMR system: a new software suite for macromolecular structure determination","volume":"54","author":"Brunger","year":"1998","journal-title":"Acta Crystallogr. 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