{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T21:05:11Z","timestamp":1757451911198,"version":"3.37.3"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,10,18]],"date-time":"2020-10-18T00:00:00Z","timestamp":1602979200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Science Center of Poland","award":["DEC-2015\/17\/N\/ST4\/03937"],"award-info":[{"award-number":["DEC-2015\/17\/N\/ST4\/03937"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The majority of the proteins in living organisms occur as homo- or hetero-multimeric structures. Although there are many tools to predict the structures of single-chain proteins or protein complexes with small ligands, peptide\u2013protein and protein\u2013protein docking is more challenging. In this work, we utilized multiplexed replica-exchange molecular dynamics (MREMD) simulations with the physics-based heavily coarse-grained UNRES model, which provides more than a 1000-fold simulation speed-up compared with all-atom approaches to predict structures of protein complexes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present a new protein\u2013protein and peptide\u2013protein docking functionality of the UNRES package, which includes a variable degree of conformational flexibility. UNRES-Dock protocol was tested on a set of 55 complexes with size from 43 to 587 amino-acid residues, showing that structures of the complexes can be predicted with good quality, if the sampling of the conformational space is sufficient, especially for flexible peptide\u2013protein systems. The developed automatized protocol has been implemented in the standalone UNRES package and in the UNRES server.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>UNRES server: http:\/\/unres-server.chem.ug.edu.pl; UNRES package and data used in testing of UNRES-Dock: http:\/\/unres.pl.<\/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\/btaa897","type":"journal-article","created":{"date-parts":[[2020,10,6]],"date-time":"2020-10-06T11:39:37Z","timestamp":1601984377000},"page":"1613-1615","source":"Crossref","is-referenced-by-count":29,"title":["UNRES-Dock\u2014protein\u2013protein and peptide\u2013protein docking by coarse-grained replica-exchange MD simulations"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9710-7837","authenticated-orcid":false,"given":"Pawe\u0142","family":"Krupa","sequence":"first","affiliation":[{"name":"Faculty of Chemistry, University of Gda\u0144sk , Gda\u0144sk 80-308, Poland"},{"name":"Institute of Physics, Polish Academy of Sciences , Warsaw 02-668, Poland"}]},{"given":"Agnieszka S","family":"Karczy\u0144ska","sequence":"additional","affiliation":[{"name":"Faculty of Chemistry, University of Gda\u0144sk , Gda\u0144sk 80-308, Poland"},{"name":"University of Grenoble Alpes , Inria, CNRS, Grenoble INP, LJK, Grenoble 38000, France"}]},{"given":"Magdalena A","family":"Mozolewska","sequence":"additional","affiliation":[{"name":"Institute of Computer Science, Polish Academy of Sciences , Warsaw 01-248, Poland"}]},{"given":"Adam","family":"Liwo","sequence":"additional","affiliation":[{"name":"Faculty of Chemistry, University of Gda\u0144sk , Gda\u0144sk 80-308, Poland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0294-3403","authenticated-orcid":false,"given":"Cezary","family":"Czaplewski","sequence":"additional","affiliation":[{"name":"Faculty of Chemistry, University of Gda\u0144sk , Gda\u0144sk 80-308, Poland"}]}],"member":"286","published-online":{"date-parts":[[2020,10,18]]},"reference":[{"key":"2023051709443533100_btaa897-B1","doi-asserted-by":"crossref","first-page":"W304","DOI":"10.1093\/nar\/gky328","article-title":"UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics","volume":"46","author":"Czaplewski","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023051709443533100_btaa897-B2","doi-asserted-by":"crossref","first-page":"14936","DOI":"10.1073\/pnas.1313316110","article-title":"Lessons from application of the UNRES force field to predictions of structures of CASP10 targets","volume":"110","author":"He","year":"2013","journal-title":"Proc. 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