{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T14:38:15Z","timestamp":1776782295336,"version":"3.51.2"},"reference-count":49,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2015,10,27]],"date-time":"2015-10-27T00:00:00Z","timestamp":1445904000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004415","type":"journal-article","created":{"date-parts":[[2015,10,27]],"date-time":"2015-10-27T18:41:23Z","timestamp":1445971283000},"page":"e1004415","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":82,"title":["ENCORE: Software for Quantitative Ensemble Comparison"],"prefix":"10.1371","volume":"11","author":[{"given":"Matteo","family":"Tiberti","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elena","family":"Papaleo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tone","family":"Bengtsen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wouter","family":"Boomsma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kresten","family":"Lindorff-Larsen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2015,10,27]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1038\/nature03199","article-title":"Simultaneous determination of protein structure and dynamics","volume":"433","author":"K Lindorff-Larsen","year":"2005","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1038\/nsmb0306-184","article-title":"Is one solution good enough?","volume":"13","author":"N Furnham","year":"2006","journal-title":"Nat Struct Mol Biol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.sbi.2014.07.005","article-title":"E pluribus unum, no more: from one crystal, many conformations","volume":"28C","author":"RA Woldeyes","year":"2014","journal-title":"Curr Opin Struct Biol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1110\/ps.03328504","article-title":"Sensitivity and selectivity in protein structure comparison","volume":"13","author":"ML Sierk","year":"2004","journal-title":"Protein Sci"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1002\/prot.10250","article-title":"Efficient RMSD measures for the comparison of two molecular ensembles. Root-mean-square deviation","volume":"50","author":"R Br\u00fcschweiler","year":"2003","journal-title":"Proteins"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"e4203","DOI":"10.1371\/journal.pone.0004203","article-title":"Similarity measures for protein ensembles","volume":"4","author":"K Lindorff-Larsen","year":"2009","journal-title":"PLoS One"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"213","DOI":"10.3390\/e14020213","article-title":"Quantitative Comparison of Conformational Ensembles","volume":"14","author":"KC Wolfe","year":"2012","journal-title":"Entropy"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"5148","DOI":"10.1021\/ct400529k","article-title":"Predicting the Thermodynamics and Kinetics of Helix Formation in a Cyclic Peptide Model","volume":"9","author":"JM Damas","year":"2013","journal-title":"J Chem Theory Comput"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"2162","DOI":"10.1016\/j.str.2013.09.014","article-title":"Phosphorylation drives a dynamic switch in serine\/arginine-rich proteins","volume":"21","author":"S Xiang","year":"2013","journal-title":"Structure"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nmeth.2921","article-title":"Measuring similarity between dynamic ensembles of biomolecules","volume":"11","author":"S Yang","year":"2014","journal-title":"Nat Methods"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1021\/ct300008d","article-title":"Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion","volume":"8","author":"CL McClendon","year":"2012","journal-title":"J Chem Theory Comput"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e10262","DOI":"10.1371\/journal.pone.0010262","article-title":"Fast mapping of global protein folding states by multivariate NMR: a GPS for proteins","volume":"5","author":"A Malmendal","year":"2010","journal-title":"PLoS One"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nmeth.2453","article-title":"Comprehensive macromolecular conformations mapped by quantitative SAXS analyses","volume":"10","author":"GL Hura","year":"2013","journal-title":"Nat Methods"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"2319","DOI":"10.1002\/jcc.21787","article-title":"MDAnalysis: A toolkit for the analysis of molecular dynamics simulations","volume":"32","author":"N Michaud-Agrawal","year":"2011","journal-title":"J Comput Chem"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"e32131","DOI":"10.1371\/journal.pone.0032131","article-title":"Systematic validation of protein force fields against experimental data","volume":"7","author":"K Lindorff-Larsen","year":"2012","journal-title":"PLoS One"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"10336","DOI":"10.1021\/ja200461n","article-title":"Weak long-range correlated motions in a surface patch of ubiquitin involved in molecular recognition","volume":"133","author":"RB Fenwick","year":"2011","journal-title":"J Am Chem Soc"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1126\/science.1187409","article-title":"Atomic-level characterization of the structural dynamics of proteins","volume":"330","author":"DE Shaw","year":"2010","journal-title":"Science"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1109\/MCSE.2010.118","article-title":"Cython: The best of both the worlds","volume":"13","author":"S Behnel","year":"2010","journal-title":"Comput Sci Eng"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1126\/science.1136800","article-title":"Clustering by passing messages between data points","volume":"315","author":"BJ Frey","year":"2007","journal-title":"Science"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"15869","DOI":"10.1073\/pnas.242424399","article-title":"A self-organizing principle for learning nonlinear manifolds","volume":"99","author":"DK Agrafiotis","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"16916","DOI":"10.1073\/pnas.1018393108","article-title":"Tree preserving embedding","volume":"108","author":"AD Shieh","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1016\/S0022-2836(83)80306-4","article-title":"Molecular dynamics of native protein. II. Analysis and nature of motion","volume":"168","author":"M Levitt","year":"1983","journal-title":"J Mol Biol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.tibs.2004.11.008","article-title":"Protein folding and the organization of the protein topology universe","volume":"30","author":"K Lindorff-Larsen","year":"2005","journal-title":"Trends Biochem Sci"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"042103","DOI":"10.1103\/PhysRevE.63.042103","article-title":"Relative entropy: Free energy associated with equilibrium fluctuations and nonequilibrium deviations","volume":"63","author":"H Qian","year":"2001","journal-title":"Phys Rev E"},{"key":"ref25","first-page":"16","author":"ME Wall","year":"2006"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"e0121114","DOI":"10.1371\/journal.pone.0121114","article-title":"Comparing MD force-fields in the essential subspace","volume":"10","author":"F Mart\u00edn-Garc\u00eda","year":"2015","journal-title":"PLoS One"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"031910","DOI":"10.1103\/PhysRevE.65.031910","article-title":"Convergence of sampling in protein simulations","volume":"65","author":"B Hess","year":"2002","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"8662","DOI":"10.1039\/c2cp23961b","article-title":"Will molecular dynamics simulations of proteins ever reach equilibrium?","volume":"14","author":"S Genheden","year":"2012","journal-title":"Phys Chem Chem Phys"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1007\/s10822-011-9497-y","article-title":"Let\u2019s get honest about sampling","volume":"26","author":"DL Mobley","year":"2012","journal-title":"J Comput Aided Mol Des"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1707","DOI":"10.1016\/S0006-3495(96)79372-4","article-title":"The consistency of large concerted motions in proteins in molecular dynamics simulations","volume":"71","author":"BL De Groot","year":"1996","journal-title":"Biophys J"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1002\/prot.340100407","article-title":"Exploration of disorder in protein structures by X-ray restrained molecular dynamics","volume":"10","author":"J Kuriyan","year":"1991","journal-title":"Proteins"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/0009-2614(89)87249-5","article-title":"Time-dependent distance restraints in molecular dynamics simulations","volume":"157","author":"A Torda","year":"1989","journal-title":"Chem Phys Lett"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"e79439","DOI":"10.1371\/journal.pone.0079439","article-title":"Inference of structure ensembles of flexible biomolecules from sparse, averaged data","volume":"8","author":"S Olsson","year":"2013","journal-title":"PLoS One"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1016\/j.bpj.2014.02.009","article-title":"Bayesian energy landscape tilting: towards concordant models of molecular ensembles","volume":"106","author":"KA Beauchamp","year":"2014","journal-title":"Biophys J"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"3445","DOI":"10.1021\/ct300112v","article-title":"On the Use of Experimental Observations to Bias Simulated Ensembles","volume":"8","author":"JW Pitera","year":"2012","journal-title":"J Chem Theory Comput"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"084107","DOI":"10.1063\/1.4792208","article-title":"On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method","volume":"138","author":"B Roux","year":"2013","journal-title":"J Chem Phys"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"094112","DOI":"10.1063\/1.4793625","article-title":"Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle","volume":"138","author":"A Cavalli","year":"2013","journal-title":"J Chem Phys"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"e1003406","DOI":"10.1371\/journal.pcbi.1003406","article-title":"Combining experiments and simulations using the maximum entropy principle","volume":"10","author":"W Boomsma","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"10901","DOI":"10.1073\/pnas.0511156103","article-title":"Relation between native ensembles and experimental structures of proteins","volume":"103","author":"RB Best","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1126\/science.1157092","article-title":"Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution","volume":"320","author":"OF Lange","year":"2008","journal-title":"Science"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1007\/s10858-006-9117-7","article-title":"The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins","volume":"37","author":"B Richter","year":"2007","journal-title":"J Biomol NMR"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1007\/s10858-012-9644-3","article-title":"Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings","volume":"53","author":"RW Montalvao","year":"2012","journal-title":"J Biomol NMR"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"3752","DOI":"10.1021\/ja4132642","article-title":"Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase","volume":"136","author":"AS Maltsev","year":"2014","journal-title":"J Am Chem Soc"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"9885","DOI":"10.1073\/pnas.0603553103","article-title":"Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction","volume":"103","author":"P Das","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1093\/bioinformatics\/btr692","article-title":"Fast large-scale clustering of protein structures using Gauss integrals","volume":"28","author":"T Harder","year":"2012","journal-title":"Bioinformatics"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"2184","DOI":"10.1093\/bioinformatics\/btn396","article-title":"Mixture models for protein structure ensembles","volume":"24","author":"M Hirsch","year":"2008","journal-title":"Bioinformatics"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1126\/science.1208351","article-title":"How fast-folding proteins fold","volume":"334","author":"K Lindorff-Larsen","year":"2011","journal-title":"Science"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.sbi.2014.04.002","article-title":"Markov state models of biomolecular conformational dynamics","volume":"25","author":"JD Chodera","year":"2014","journal-title":"Curr Opin Struct Biol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"5716","DOI":"10.1021\/ct500827g","article-title":"Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State Models","volume":"10","author":"VA Voelz","year":"2014","journal-title":"J Chem Theory Comput"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004415","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T10:38:24Z","timestamp":1589020704000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004415"}},"subtitle":[],"editor":[{"given":"Bert L.","family":"de Groot","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,10,27]]},"references-count":49,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2015,10,27]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004415","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,10,27]]}}}