{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T11:20:13Z","timestamp":1782818413849,"version":"3.54.5"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,11,7]],"date-time":"2016-11-07T00:00:00Z","timestamp":1478476800000},"content-version":"vor","delay-in-days":920,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles.<\/jats:p>\n               <jats:p>Results: Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting protein regions that undergo conformational changes as well as the extent of such changes.<\/jats:p>\n               <jats:p>Availability and implementation: The CABS-flex is freely available to all users at http:\/\/biocomp.chem.uw.edu.pl\/CABSflex .<\/jats:p>\n               <jats:p>Contact : sekmi@chem.uw.edu.pl<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu184","type":"journal-article","created":{"date-parts":[[2014,4,16]],"date-time":"2014-04-16T04:18:33Z","timestamp":1397621913000},"page":"2150-2154","source":"Crossref","is-referenced-by-count":96,"title":["CABS-flex predictions of protein flexibility compared with NMR ensembles"],"prefix":"10.1093","volume":"30","author":[{"given":"Michal","family":"Jamroz","sequence":"first","affiliation":[{"name":"Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrzej","family":"Kolinski","sequence":"additional","affiliation":[{"name":"Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian","family":"Kmiecik","sequence":"additional","affiliation":[{"name":"Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,5,2]]},"reference":[{"key":"2023012711332613500_btu184-B1","doi-asserted-by":"crossref","first-page":"W406","DOI":"10.1093\/nar\/gkt462","article-title":"CABS-fold: server for the de novo and consensus-based prediction of protein structure","volume":"41","author":"Blaszczyk","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012711332613500_btu184-B2","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1002\/prot.22081","article-title":"In pursuit of virtual lead optimization: the role of the receptor structure and ensembles in accurate docking","volume":"73","author":"Bolstad","year":"2008","journal-title":"Proteins"},{"key":"2023012711332613500_btu184-B3","doi-asserted-by":"crossref","first-page":"8225","DOI":"10.1021\/ja0709728","article-title":"Exploring experimental sources of multiple protein conformations in structure-based drug design","volume":"129","author":"Damm","year":"2007","journal-title":"J. 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