{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T02:55:57Z","timestamp":1775789757588,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2022,1,3]],"date-time":"2022-01-03T00:00:00Z","timestamp":1641168000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI1564606"],"award-info":[{"award-number":["DBI1564606"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IIS1901191"],"award-info":[{"award-number":["IIS1901191"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI2030790"],"award-info":[{"award-number":["DBI2030790"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MTM2025426"],"award-info":[{"award-number":["MTM2025426"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM136422"],"award-info":[{"award-number":["GM136422"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["S10OD026825"],"award-info":[{"award-number":["S10OD026825"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI134678"],"award-info":[{"award-number":["AI134678"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Accurate and efficient predictions of protein structures play an important role in understanding their functions. Iterative Threading Assembly Refinement (I-TASSER) is one of the most successful and widely used protein structure prediction methods in the recent community-wide CASP experiments. Yet, the computational efficiency of I-TASSER is one of the limiting factors that prevent its application for large-scale structure modeling.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present I-TASSER for Graphics Processing Units (GPU-I-TASSER), a GPU accelerated I-TASSER protein structure prediction tool for fast and accurate protein structure prediction. Our implementation is based on OpenACC parallelization of the replica-exchange Monte Carlo simulations to enhance the speed of I-TASSER by extending its capabilities to the GPU architecture. On a benchmark dataset of 71 protein structures, GPU-I-TASSER achieves on average a 10\u00d7 speedup with comparable structure prediction accuracy compared to the CPU version of the I-TASSER.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The complete source code for GPU-I-TASSER can be downloaded and used without restriction from https:\/\/zhanggroup.org\/GPU-I-TASSER\/.<\/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\/btab871","type":"journal-article","created":{"date-parts":[[2021,12,28]],"date-time":"2021-12-28T20:28:16Z","timestamp":1640723296000},"page":"1754-1755","source":"Crossref","is-referenced-by-count":13,"title":["GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool"],"prefix":"10.1093","volume":"38","author":[{"given":"Elijah A","family":"MacCarthy","sequence":"first","affiliation":[{"name":"Department of Mathematics, Lane College , Jackson, TN 38301, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7290-1324","authenticated-orcid":false,"given":"Chengxin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine & Bioinformatics, University of Michigan , Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine & Bioinformatics, University of Michigan , Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7443-1928","authenticated-orcid":false,"given":"Dukka B","family":"KC","sequence":"additional","affiliation":[{"name":"Computer Science Department, Michigan Technological University , Houghton, MI 49931, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,1,3]]},"reference":[{"key":"2023020201174515200_btab871-B1","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1126\/science.abj8754","article-title":"Accurate prediction of protein structures and interactions using a three-track neural network","volume":"373","author":"Baek","year":"2021","journal-title":"Science"},{"key":"2023020201174515200_btab871-B2","doi-asserted-by":"crossref","first-page":"1638","DOI":"10.1016\/j.cpc.2011.04.012","article-title":"Massively parallelized replica-exchange simulations of polymers on GPUs","volume":"182","author":"Gross","year":"2011","journal-title":"Comput. Phys. Commun"},{"key":"2023020201174515200_btab871-B3","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2023020201174515200_btab871-B4","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1007\/978-1-4939-0366-5_2","article-title":"RaptorX server: a resource for template-based protein structure modeling","volume":"1137","author":"Kallberg","year":"2014","journal-title":"Methods Mol. Biol"},{"key":"2023020201174515200_btab871-B5","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1002\/prot.25823","article-title":"Critical assessment of methods of protein structure prediction (CASP)-Round XIII","volume":"87","author":"Kryshtafovych","year":"2019","journal-title":"Proteins"},{"key":"2023020201174515200_btab871-B6","doi-asserted-by":"crossref","first-page":"1607","DOI":"10.1002\/prot.26237","article-title":"Critical assessment of methods of protein structure prediction (CASP)-Round XIV","volume":"89","author":"Kryshtafovych","year":"2021","journal-title":"Proteins"},{"key":"2023020201174515200_btab871-B7","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1063\/1.1699114","article-title":"Equation of state calculations by fast computing machines","volume":"21","author":"Metropolis","year":"1953","journal-title":"J. Chem. Phys"},{"key":"2023020201174515200_btab871-B8","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/S0076-6879(04)83004-0","article-title":"Protein structure prediction using Rosetta","volume":"383","author":"Rohl","year":"2004","journal-title":"Methods Enzymol"},{"key":"2023020201174515200_btab871-B9","doi-asserted-by":"crossref","first-page":"1715","DOI":"10.1002\/prot.24065","article-title":"Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field","volume":"80","author":"Xu","year":"2012","journal-title":"Proteins"},{"key":"2023020201174515200_btab871-B10","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/nmeth.3213","article-title":"The I-TASSER Suite: protein structure and function prediction","volume":"12","author":"Yang","year":"2015","journal-title":"Nat. Methods"},{"key":"2023020201174515200_btab871-B11","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1002\/prot.20264","article-title":"Scoring function for automated assessment of protein structure template quality","volume":"57","author":"Zhang","year":"2004","journal-title":"Proteins"},{"key":"2023020201174515200_btab871-B12","doi-asserted-by":"crossref","first-page":"W429","DOI":"10.1093\/nar\/gkz384","article-title":"LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins","volume":"47","author":"Zheng","year":"2019","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab871\/42077557\/btab871.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/6\/1754\/49008719\/btab871.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/6\/1754\/49008719\/btab871.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:38:18Z","timestamp":1675309098000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/6\/1754\/6493207"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,1,3]]},"references-count":12,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2022,3,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab871","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,3,15]]},"published":{"date-parts":[[2022,1,3]]}}}