{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T04:22:11Z","timestamp":1772684531608,"version":"3.50.1"},"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2014,2,20]],"date-time":"2014-02-20T00:00:00Z","timestamp":1392854400000},"content-version":"unspecified","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.1003406","type":"journal-article","created":{"date-parts":[[2014,2,20]],"date-time":"2014-02-20T21:57:38Z","timestamp":1392933458000},"page":"e1003406","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":187,"title":["Combining Experiments and Simulations Using the Maximum Entropy Principle"],"prefix":"10.1371","volume":"10","author":[{"given":"Wouter","family":"Boomsma","sequence":"first","affiliation":[]},{"given":"Jesper","family":"Ferkinghoff-Borg","sequence":"additional","affiliation":[]},{"given":"Kresten","family":"Lindorff-Larsen","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,2,20]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1103\/PhysRev.106.620","article-title":"Information theory and statistical mechanics","volume":"106","author":"ET Jaynes","year":"1957","journal-title":"Phys Rev"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"e1002922","DOI":"10.1371\/journal.pcbi.1002922","article-title":"Stimulus-dependent maximum entropy models of neural population codes","volume":"9","author":"E Granot-Atedgi","year":"2013","journal-title":"PLOS Comput Biol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"e6522","DOI":"10.1371\/journal.pone.0006522","article-title":"Maximum entropy reconstructions of dynamic signaling networks from quantitative proteomics data","volume":"4","author":"JW Locasale","year":"2009","journal-title":"PLOS One"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"8383","DOI":"10.1021\/jp2114994","article-title":"A new multiscale algorithm and its application to coarse-grained peptide models for self-assembly","volume":"116","author":"SP Carmichael","year":"2012","journal-title":"J Phys Chem B"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1214\/lnms\/1215455556","article-title":"Correlated mutations in models of protein sequences: phylogenetic and structural effects","volume":"33","author":"AS Lapedes","year":"1999","journal-title":"Lect Notes Monogr Ser"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"E1293","DOI":"10.1073\/pnas.1111471108","article-title":"Direct-coupling analysis of residue coevolution captures native contacts across many protein families","volume":"108","author":"F Morcos","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.sbi.2009.03.004","article-title":"Long-timescale molecular dynamics simulations of protein structure and function","volume":"19","author":"JL Klepeis","year":"2009","journal-title":"Curr Opin Struct Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1529\/biophysj.107.108241","article-title":"Experimental parameterization of an energy function for the simulation of unfolded proteins","volume":"94","author":"AB Norgaard","year":"2008","journal-title":"Biophys J"},{"key":"ref9","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":"ref10","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":"ref11","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":"ref12","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","article-title":"A mathematical theory of communication","volume":"27","author":"CE Shannon","year":"1948","journal-title":"Bell System Technical Journal"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1214\/aoms\/1177729694","article-title":"On information and sufficiency","volume":"22","author":"S Kullback","year":"1951","journal-title":"Ann Math Statist"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1109\/TSSC.1968.300117","article-title":"Prior probabilities","volume":"4","author":"ET Jaynes","year":"1968","journal-title":"IEEE Trans Syst Sci Cybern"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1007\/BF01106578","article-title":"A new theorem of information theory","volume":"1","author":"A Hobson","year":"1969","journal-title":"J Stat Phys"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1109\/TIT.1980.1056144","article-title":"Axiomatic derivation of the principle of maximum entropy and the principle of minimum cross-entropy","volume":"26","author":"J Shore","year":"1980","journal-title":"IEEE Trans Inf Theory"},{"key":"ref17","unstructured":"Jaynes E (1979) Where do we stand on maximum entropy? In: Levine R, Tribus M, editors. The Maximum Entropy Formalism. Cambridge, MA: MIT Press. pp. 1\u2013104."},{"key":"ref18","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":"ref19","unstructured":"Leaver-Fay A, O&apos;Meara MJ, Tyka M, Jacak R, Song Y, <etal>et al<\/etal>.. (2013) Chapter six - scientific benchmarks for guiding macromolecular energy function improvement. In: Keating AE, editor. Methods in Protein Design, Academic Press, Volume 523 of Methods in Enzymology. pp. 109\u2013143."},{"key":"ref20","doi-asserted-by":"crossref","first-page":"9004","DOI":"10.1021\/jp901540t","article-title":"Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides","volume":"113","author":"RB Best","year":"2009","journal-title":"J Phys Chem B"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"2483","DOI":"10.1002\/jcc.23069","article-title":"Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers","volume":"33","author":"MD Tyka","year":"2012","journal-title":"J Comput Chem"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"2071","DOI":"10.1002\/prot.24098","article-title":"Refinement of protein structure homology models via long, all-atom molecular dynamics simulations","volume":"80","author":"A Raval","year":"2012","journal-title":"Proteins"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1126\/science.1110428","article-title":"Inferential structure determination","volume":"309","author":"W Rieping","year":"2005","journal-title":"Science"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1756","DOI":"10.1073\/pnas.0506412103","article-title":"Weighting of experimental evidence in macromolecular structure determination","volume":"103","author":"M Habeck","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.sbi.2007.01.002","article-title":"Determination of conformationally heterogeneous states of proteins","volume":"17","author":"M Vendruscolo","year":"2007","journal-title":"Curr Opin Struct Biol"},{"key":"ref26","doi-asserted-by":"crossref","unstructured":"Scheek RM, Torda AE, Kemmink J, van Gunsteren WF (1991) Structure determination by NMR: The modeling of NMR parameters as ensemble averages. In: Hoch JC, Poulsen FM, Redfield C, editors. Computational aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy. New York: Plenum Press. pp. 209\u2013217.","DOI":"10.1007\/978-1-4757-9794-7_15"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"8792","DOI":"10.1021\/bi00448a017","article-title":"A dynamic model for the structure of acyl carrier protein in solution","volume":"28","author":"Y Kim","year":"1989","journal-title":"Biochemistry"},{"key":"ref28","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":"ref29","doi-asserted-by":"crossref","first-page":"1040","DOI":"10.1016\/j.str.2007.06.019","article-title":"Ensemble refinement of protein crystal structures: validation and application","volume":"15","author":"EJ Levin","year":"2007","journal-title":"Structure"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"e00311","DOI":"10.7554\/eLife.00311","article-title":"Modelling dynamics in protein crystal structures by ensemble refinement","volume":"1","author":"BT Burnley","year":"2012","journal-title":"eLife"},{"key":"ref31","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":"ref32","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":"ref33","doi-asserted-by":"crossref","first-page":"4733","DOI":"10.1021\/jp3110369","article-title":"Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron\u2013electron resonance spectroscopy","volume":"117","author":"B Roux","year":"2013","journal-title":"J Phys Chem B"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"3291","DOI":"10.1021\/ja039250g","article-title":"Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme A binding protein","volume":"126","author":"K Lindorff-Larsen","year":"2004","journal-title":"J Am Chem Soc"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"2913","DOI":"10.1016\/j.bpj.2011.05.009","article-title":"Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state nmr observables","volume":"100","author":"S Jo","year":"2011","journal-title":"Biophys J"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1021\/ja044834j","article-title":"Mapping long-range interactions in \u03b1-synuclein using spin-label NMR and ensemble molecular dynamics simulations","volume":"127","author":"MM Dedmon","year":"2005","journal-title":"J Am Chem Soc"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1007\/s10858-006-9117-7","article-title":"The MUMO (minimal underrestraining 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":"ref38","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":"ref39","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1126\/science.271.5245.72","article-title":"Direct observation of protein salvation and discrete disorder with experimental crystallographic phases","volume":"271","author":"FT Burling","year":"1996","journal-title":"Science"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.sbi.2007.12.007","article-title":"Molecular simulation as an aid to experimentalists","volume":"18","author":"WF van Gunsteren","year":"2008","journal-title":"Curr Opin Struct Biol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1107\/S0108767384000866","article-title":"Maximum entropy and the foundations of direct methods","volume":"40","author":"G Bricogne","year":"1984","journal-title":"Acta Crystallogr A"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.str.2010.10.006","article-title":"SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions","volume":"19","author":"B R\u00f3z`ycki","year":"2011","journal-title":"Structure"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1023\/A:1008349424452","article-title":"Maximum entropy approach to the determination of solution conformation of exible polypeptides by global conformational analysis and NMR spectroscopy \u2013 application to DNS<sup>1<\/sup>-c-[D-A<sub>2<\/sub>bu<sup>2<\/sup>, Trp<sup>4<\/sup>, Leu<sup>5<\/sup>]-enkephalin and DNS<sup>1<\/sup>-c-[D-A<sub>2<\/sub>bu<sup>2<\/sup>, Trp<sup>4<\/sup>, D-Leu<sup>5<\/sup>] enkephalin","volume":"15","author":"M Groth","year":"1999","journal-title":"J Biomol NMR"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1007\/s10858-007-9150-1","article-title":"Maximum entropy reconstruction of joint <italic>\u03c6<\/italic>, <italic>\u03c8<\/italic>-distribution with a coil-library prior: the backbone conformation of the peptide hormone motilin in aqueous solution from <italic>\u03c6<\/italic> and <italic>\u03c8<\/italic>-dependent J-couplings","volume":"38","author":"T Massad","year":"2007","journal-title":"J Biomol NMR"},{"key":"ref45","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":"ref46","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1287\/opre.27.6.1188","article-title":"Technical note \u2013 a generalized maximum entropy principle","volume":"27","author":"MU Thomas","year":"1979","journal-title":"Oper Res"},{"key":"ref47","unstructured":"Golan A, Judge G, Miller D (1996) Maximum entropy econometrics: robust estimation with limited data. Series in financial economics and quantitative analysis. San Francisco: Wiley. 307 pp."},{"key":"ref48","first-page":"1217","article-title":"Maximum entropy density estimation with generalized regularization and an application to species distribution modeling","volume":"8","author":"M Dud\u00edk","year":"2007","journal-title":"J Mach Learn Res"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1111\/j.2517-6161.1992.tb01864.x","article-title":"Maximum entropy and the nearly black object","volume":"54","author":"DL Donoho","year":"1992","journal-title":"J R Stat Soc Series B Stat Methodol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1038\/272686a0","article-title":"Image reconstruction from incomplete and noisy data","volume":"272","author":"S Gull","year":"1978","journal-title":"Nature"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"e79439","DOI":"10.1371\/journal.pone.0079439","article-title":"Inference of structure ensembles from sparse, averaged data","volume":"8","author":"S Olsson","year":"2013","journal-title":"PLOS One"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1021\/ct300826t","article-title":"Systematic parametrization of polarizable force fields from quantum chemistry data","volume":"9","author":"LP Wang","year":"2012","journal-title":"J Chem Theory Comput"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/j.jmr.2011.08.039","article-title":"Generative probabilistic models extend the scope of inferential structure determination","volume":"213","author":"S Olsson","year":"2011","journal-title":"Journal of Magnetic Resonance"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003406","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,24]],"date-time":"2024-05-24T12:14:10Z","timestamp":1716552850000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003406"}},"subtitle":[],"editor":[{"given":"Michael","family":"Levitt","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,2,20]]},"references-count":53,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2014,2,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003406","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,2,20]]}}}