{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T22:00:37Z","timestamp":1774648837582,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,6,20]],"date-time":"2023-06-20T00:00:00Z","timestamp":1687219200000},"content-version":"vor","delay-in-days":19,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004281","name":"National Science Centre","doi-asserted-by":"publisher","award":["UMO-2021\/40\/Q\/ST4\/00035"],"award-info":[{"award-number":["UMO-2021\/40\/Q\/ST4\/00035"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The UNited RESisdue (UNRES) package for coarse-grained simulations, which has recently been optimized to treat large protein systems, has been implemented on Graphical Processor Units (GPUs). An over 100-time speed-up of the GPU code (run on an NVIDIA A100) with respect to the sequential code and an 8.5 speed-up with respect to the parallel Open Multi-Processing (OpenMP) code (run on 32 cores of 2 AMD EPYC 7313 Central Processor Units (CPUs)) has been achieved for large proteins (with size over 10\u00a0000 residues). Due to the averaging over the fine-grain degrees of freedom, 1 time unit of UNRES simulations is equivalent to about 1000 time units of laboratory time; therefore, millisecond time scale of large protein systems can be reached with the UNRES-GPU code.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code of UNRES-GPU along with the benchmarks used for tests is available at https:\/\/projects.task.gda.pl\/eurohpcpl-public\/unres.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad391","type":"journal-article","created":{"date-parts":[[2023,6,20]],"date-time":"2023-06-20T15:15:02Z","timestamp":1687274102000},"source":"Crossref","is-referenced-by-count":8,"title":["UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4472-6116","authenticated-orcid":false,"given":"Krzysztof M","family":"Ocetkiewicz","sequence":"first","affiliation":[{"name":"Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gda\u0144sk University of Technology, Fahrenheit Union of Universities in Gda\u0144sk , Gda\u0144sk 80-233, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0294-3403","authenticated-orcid":false,"given":"Cezary","family":"Czaplewski","sequence":"additional","affiliation":[{"name":"Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gda\u0144sk University of Technology, Fahrenheit Union of Universities in Gda\u0144sk , Gda\u0144sk 80-233, Poland"},{"name":"Faculty of Chemistry, University of Gda\u0144sk, Fahrenheit Union of Universities in Gda\u0144sk , Gda\u0144sk 80-309, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0436-6264","authenticated-orcid":false,"given":"Henryk","family":"Krawczyk","sequence":"additional","affiliation":[{"name":"Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gda\u0144sk University of Technology, Fahrenheit Union of Universities in Gda\u0144sk , Gda\u0144sk 80-233, Poland"},{"name":"Faculty of Electronics, Telecommunications and Informatics, Gda\u0144sk University of Technology, Fahrenheit Union of Universities in Gda\u0144sk , Gda\u0144sk 80-233, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8390-8473","authenticated-orcid":false,"given":"Agnieszka G","family":"Lipska","sequence":"additional","affiliation":[{"name":"Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gda\u0144sk University of Technology, Fahrenheit Union of Universities in Gda\u0144sk , Gda\u0144sk 80-233, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6942-2226","authenticated-orcid":false,"given":"Adam","family":"Liwo","sequence":"additional","affiliation":[{"name":"Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gda\u0144sk University of Technology, Fahrenheit Union of Universities in Gda\u0144sk , Gda\u0144sk 80-233, Poland"},{"name":"Faculty of Chemistry, University of Gda\u0144sk, Fahrenheit Union of Universities in Gda\u0144sk , Gda\u0144sk 80-309, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2975-9339","authenticated-orcid":false,"given":"Jerzy","family":"Proficz","sequence":"additional","affiliation":[{"name":"Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gda\u0144sk University of Technology, Fahrenheit Union of Universities in Gda\u0144sk , Gda\u0144sk 80-233, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2426-3644","authenticated-orcid":false,"given":"Adam K","family":"Sieradzan","sequence":"additional","affiliation":[{"name":"Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gda\u0144sk University of Technology, Fahrenheit Union of Universities in Gda\u0144sk , Gda\u0144sk 80-233, Poland"},{"name":"Faculty of Chemistry, University of Gda\u0144sk, Fahrenheit Union of Universities in Gda\u0144sk , Gda\u0144sk 80-309, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4918-9196","authenticated-orcid":false,"given":"Pawe\u0142","family":"Czarnul","sequence":"additional","affiliation":[{"name":"Faculty of Electronics, Telecommunications and Informatics, Gda\u0144sk University of Technology, Fahrenheit Union of Universities in Gda\u0144sk , Gda\u0144sk 80-233, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,6,20]]},"reference":[{"key":"2023062908344936800_btad391-B1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"Gromacs: high performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1\u20132","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"2023062908344936800_btad391-B2","doi-asserted-by":"crossref","first-page":"108008","DOI":"10.1016\/j.jmgm.2021.108008","article-title":"Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment","volume":"108","author":"Antoniak","year":"2021","journal-title":"J Mol Graph Model"},{"key":"2023062908344936800_btad391-B3","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1021\/ct800397z","article-title":"Application of multiplexing replica exchange molecular dynamics method to the UNRES force field: tests with \u03b1 and \u03b1+\u03b2 proteins","volume":"5","author":"Czaplewski","year":"2009","journal-title":"J Chem Theory Comput"},{"key":"2023062908344936800_btad391-B4","doi-asserted-by":"crossref","first-page":"510","DOI":"10.31577\/cai_2020_3_510","article-title":"Investigation of parallel data processing using hybrid high performance CPU + GPU systems and CUDA streams","volume":"39","author":"Czarnul","year":"2020","journal-title":"Comput Informatics"},{"key":"2023062908344936800_btad391-B5","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/S0009-2614(97)01198-6","article-title":"Parallel tempering algorithm for conformational studies of biological molecules","volume":"281","author":"Hansmann","year":"1997","journal-title":"Chem Phys Lett"},{"key":"2023062908344936800_btad391-B6","doi-asserted-by":"crossref","first-page":"13798","DOI":"10.1021\/jp058007w","article-title":"Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model \u03b1-helical systems","volume":"109","author":"Khalili","year":"2005","journal-title":"J Phys Chem B"},{"key":"2023062908344936800_btad391-B7","doi-asserted-by":"crossref","first-page":"7898","DOI":"10.1021\/acs.chemrev.6b00163","article-title":"Coarse-grained protein models and their applications","volume":"116","author":"Kmiecik","year":"2016","journal-title":"Chem Rev"},{"key":"2023062908344936800_btad391-B8","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1143\/JPSJ.17.1100","article-title":"Generalized cumulant expansion method","volume":"17","author":"Kubo","year":"1962","journal-title":"J Phys Soc Jpn"},{"key":"2023062908344936800_btad391-B9","doi-asserted-by":"crossref","first-page":"2323","DOI":"10.1063\/1.1383989","article-title":"Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field","volume":"115","author":"Liwo","year":"2001","journal-title":"J Chem Phys"},{"key":"2023062908344936800_btad391-B10","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1021\/jp065380a","article-title":"Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins","volume":"111","author":"Liwo","year":"2007","journal-title":"J Phys Chem B"},{"key":"2023062908344936800_btad391-B11","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1021\/ct9004068","article-title":"Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics","volume":"6","author":"Liwo","year":"2010","journal-title":"J Chem Theory Comput"},{"key":"2023062908344936800_btad391-B12","doi-asserted-by":"crossref","first-page":"2306","DOI":"10.1007\/s00894-014-2306-5","article-title":"A unified coarse-grained model of biological macromolecules based on mean-field multipole\u2013multipole interactions","volume":"20","author":"Liwo","year":"2014","journal-title":"J Mol Model"},{"key":"2023062908344936800_btad391-B13","doi-asserted-by":"crossref","first-page":"e1008308","DOI":"10.1371\/journal.pcbi.1008308","article-title":"OpenAWSEM with Open3SPN2: a fast, flexible, and accessible framework for largescale coarse-grained biomolecular simulations","volume":"17","author":"Lu","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"2023062908344936800_btad391-B14","first-page":"63","article-title":"High performance computing with coarse grained model of biological macromolecules","volume":"5","author":"Lubecka","year":"2018","journal-title":"Supercomput Front Innov"},{"key":"2023062908344936800_btad391-B15","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1016\/S0006-3495(03)74897-8","article-title":"Multiplexed-replica exchange molecular dynamics method for protein folding simulation","volume":"84","author":"Rhee","year":"2003","journal-title":"Biophys J"},{"key":"2023062908344936800_btad391-B16","doi-asserted-by":"crossref","first-page":"124106","DOI":"10.1063\/1.4978680","article-title":"A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains","volume":"146","author":"Sieradzan","year":"2017","journal-title":"J Chem Phys"},{"key":"2023062908344936800_btad391-B17","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1002\/jcc.27026","article-title":"Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins","volume":"44","author":"Sieradzan","year":"2023","journal-title":"J Comput Chem"},{"key":"2023062908344936800_btad391-B18","doi-asserted-by":"crossref","first-page":"045103","DOI":"10.1063\/5.0014500","article-title":"ddcmd: a fully GPU-accelerated molecular dynamics program for the martini force field","volume":"153","author":"Zhang","year":"2020","journal-title":"J Chem Phys"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad391\/50657951\/btad391.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/6\/btad391\/50738091\/btad391.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/6\/btad391\/50738091\/btad391.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,29]],"date-time":"2023-06-29T08:35:18Z","timestamp":1688027718000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad391\/7203798"}},"subtitle":[],"editor":[{"given":"Arne","family":"Elofsson","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,6,1]]},"references-count":18,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2023,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad391","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,6,1]]},"published":{"date-parts":[[2023,6,1]]},"article-number":"btad391"}}