{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T07:46:35Z","timestamp":1772005595287,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2017,8,21]],"date-time":"2017-08-21T00:00:00Z","timestamp":1503273600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Accurate structural models of biological systems can be obtained by properly combining experimental data with a priori physico\u2013chemical knowledge. Here we present PLUMED-ISDB, an open-source, freely-available module of the popular PLUMED library, which enables the simultaneous determination of structure and dynamics of conformationally heterogeneous systems by integrating experimental data with a priori information. This integration is achieved using metainference, a general Bayesian framework that accounts for both noise in the data and their ensemble-averaged nature. PLUMED-ISDB implements different types of experimental data, such as several NMR observables, FRET, SAXS and cryo-electron microscopy data, and enables modelling structure and dynamics of individual proteins, protein complexes, membrane proteins, RNA and DNA, using a variety of enhanced sampling methods and resolutions of the system.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PLUMED-ISDB is freely available at www.plumed.org.<\/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\/btx529","type":"journal-article","created":{"date-parts":[[2017,8,17]],"date-time":"2017-08-17T11:09:43Z","timestamp":1502968183000},"page":"3999-4000","source":"Crossref","is-referenced-by-count":76,"title":["Integrative structural and dynamical biology with PLUMED-ISDB"],"prefix":"10.1093","volume":"33","author":[{"given":"Massimiliano","family":"Bonomi","sequence":"first","affiliation":[{"name":"Department of Chemistry, University of Cambridge, Cambridge, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9923-8590","authenticated-orcid":false,"given":"Carlo","family":"Camilloni","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Institute for Advanced Study, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany"},{"name":"Dipartimento di Bioscienze, Universit\u00e0 degli Studi di Milano, Milan, Italy"}]}],"member":"286","published-online":{"date-parts":[[2017,8,21]]},"reference":[{"key":"2023020207510808500_btx529-B1","doi-asserted-by":"crossref","first-page":"e1501177","DOI":"10.1126\/sciadv.1501177","article-title":"Metainference: a Bayesian inference method for heterogeneous systems","volume":"2","author":"Bonomi","year":"2016","journal-title":"Sci. Adv"},{"key":"2023020207510808500_btx529-B2","doi-asserted-by":"crossref","first-page":"31232","DOI":"10.1038\/srep31232","article-title":"Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics","volume":"6","author":"Bonomi","year":"2016","journal-title":"Sci. Rep"},{"key":"2023020207510808500_btx529-B3","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.sbi.2016.12.004","article-title":"Principles of protein structural ensemble determination","volume":"42","author":"Bonomi","year":"2017","journal-title":"Curr. Opin. Struct. Biol"},{"key":"2023020207510808500_btx529-B4","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1021\/jp5021824","article-title":"A tensor-free method for the structural and dynamical refinement of proteins using residual dipolar couplings","volume":"119","author":"Camilloni","year":"2015","journal-title":"J. Phys. Chem. B"},{"key":"2023020207510808500_btx529-B7","article-title":"Multi-scale Bayesian modeling of cryo-electron microscopy density maps","author":"Hanot","year":"2017","journal-title":"bioRxiv"},{"key":"2023020207510808500_btx529-B8","doi-asserted-by":"crossref","first-page":"5879","DOI":"10.1021\/ja031580d","article-title":"Ensemble approach for NMR structure refinement against H-1 paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule","volume":"126","author":"Iwahara","year":"2004","journal-title":"J. Am. Chem. Soc"},{"key":"2023020207510808500_btx529-B9","doi-asserted-by":"crossref","first-page":"13894","DOI":"10.1021\/ja903772t","article-title":"Fast and accurate predictions of protein NMR chemical shifts from interatomic distances","volume":"131","author":"Kohlhoff","year":"2009","journal-title":"J. Am. Chem. Soc"},{"key":"2023020207510808500_btx529-B10","doi-asserted-by":"crossref","first-page":"165102.","DOI":"10.1063\/1.4981211","article-title":"Metadynamic metainference: Convergence towards force field independent structural ensembles of a disordered peptide","volume":"146","author":"L\u00f6hr","year":"2017","journal-title":"J. Chem. Phys"},{"key":"2023020207510808500_btx529-B11","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1126\/science.1110428","article-title":"Inferential structure determination","volume":"309","author":"Rieping","year":"2005","journal-title":"Science"},{"key":"2023020207510808500_btx529-B12","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1016\/j.cpc.2013.09.018","article-title":"PLUMED 2: new feathers for an old bird","volume":"185","author":"Tribello","year":"2014","journal-title":"Comp. Phys. Comm"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/24\/3999\/49042146\/bioinformatics_33_24_3999.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/24\/3999\/49042146\/bioinformatics_33_24_3999.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T07:55:55Z","timestamp":1675324555000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/24\/3999\/4085774"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,8,21]]},"references-count":10,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2017,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx529","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,12,15]]},"published":{"date-parts":[[2017,8,21]]}}}