{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T19:38:39Z","timestamp":1773171519121,"version":"3.50.1"},"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2008,2,15]],"date-time":"2008-02-15T00:00:00Z","timestamp":1203033600000},"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.0040043","type":"journal-article","created":{"date-parts":[[2008,2,12]],"date-time":"2008-02-12T20:47:37Z","timestamp":1202849257000},"page":"e43","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":86,"title":["Accurate Structural Correlations from Maximum Likelihood Superpositions"],"prefix":"10.1371","volume":"4","author":[{"given":"Douglas L","family":"Theobald","sequence":"first","affiliation":[]},{"given":"Deborah S","family":"Wuttke","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2008,2,15]]},"reference":[{"key":"pcbi-0040043-b001","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1146\/annurev.pc.46.100195.001255","article-title":"Collective variable description of native protein dynamics.","volume":"46","year":"1995","journal-title":"Annu Rev Phys Chem"},{"key":"pcbi-0040043-b002","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/S0959-440X(00)00061-0","article-title":"Collective protein dynamics in relation to function.","volume":"10","year":"2000","journal-title":"Curr Opin Struct Biol"},{"key":"pcbi-0040043-b003","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/S0959-440X(99)80023-2","article-title":"Investigating protein dynamics in collective coordinate space.","volume":"9","year":"1999","journal-title":"Curr Opin Struct Biol"},{"key":"pcbi-0040043-b004","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1002\/prot.340170408","article-title":"Essential dynamics of proteins.","volume":"17","year":"1993","journal-title":"Proteins"},{"key":"pcbi-0040043-b005","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1002\/pro.5560050108","article-title":"Simulations of CRP:(cAMP) in noncyrstalline environments show a subunit transition from the open to the closed conformation.","volume":"5","year":"1996","journal-title":"Protein Sci"},{"key":"pcbi-0040043-b006","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1002\/prot.340110305","article-title":"Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations.","volume":"11","year":"1991","journal-title":"Proteins"},{"key":"pcbi-0040043-b007","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1016\/0301-0104(91)87082-7","article-title":"The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulation of melittin in water and in vacuum.","volume":"158","year":"1991","journal-title":"Chem Phys"},{"key":"pcbi-0040043-b008","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1002\/bip.360230610","article-title":"Quasi-harmonic method for studying very low frequency modes in proteins.","volume":"23","year":"1984","journal-title":"Biopolymers"},{"key":"pcbi-0040043-b009","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1111\/1467-9868.00069","article-title":"Consistency of Procrustes estimators.","volume":"59","year":"1997","journal-title":"J Roy Stat Soc B Met"},{"key":"pcbi-0040043-b010","doi-asserted-by":"crossref","unstructured":"SeberGAFWildCJ 1989 Nonlinear regression New York Wiley 768","DOI":"10.1002\/0471725315"},{"key":"pcbi-0040043-b011","first-page":"238","article-title":"Rotational superposition: A review of methods.","volume":"17","year":"1999","journal-title":"J Mol Graph Model"},{"key":"pcbi-0040043-b012","doi-asserted-by":"crossref","first-page":"18521","DOI":"10.1073\/pnas.0508445103","article-title":"Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem.","volume":"103","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0040043-b013","doi-asserted-by":"crossref","first-page":"2171","DOI":"10.1093\/bioinformatics\/btl332","article-title":"THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures.","volume":"22","year":"2006","journal-title":"Bioinformatics"},{"key":"pcbi-0040043-b014","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1126\/science.289.5481.905","article-title":"The complete atomic structure of the large ribosomal subunit at 2.4 \u00c5 resolution.","volume":"289","year":"2000","journal-title":"Science"},{"key":"pcbi-0040043-b015","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/S1097-2765(02)00570-1","article-title":"The structures of four macrolide antibiotics bound to the large ribosomal subunit.","volume":"10","year":"2002","journal-title":"Mol Cell"},{"key":"pcbi-0040043-b016","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1016\/S0022-2836(03)00668-5","article-title":"Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit.","volume":"330","year":"2003","journal-title":"J Mol Biol"},{"key":"pcbi-0040043-b017","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1016\/j.tibs.2006.07.004","article-title":"Themes in ssDNA recognition by telomere-end protection proteins.","volume":"31","year":"2006","journal-title":"Trends Biochem Sci"},{"key":"pcbi-0040043-b018","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1016\/S0969-2126(03)00183-7","article-title":"Homology among telomeric end-protection proteins.","volume":"11","year":"2003","journal-title":"Structure"},{"key":"pcbi-0040043-b019","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1146\/annurev.biophys.32.110601.142506","article-title":"Nucleic acid recognition by OB-fold proteins.","volume":"32","year":"2003","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"pcbi-0040043-b020","doi-asserted-by":"crossref","first-page":"1877","DOI":"10.1016\/j.str.2004.07.015","article-title":"Prediction of multiple tandem OB-fold domains in telomere end-binding proteins Pot1 and Cdc13.","volume":"12","year":"2004","journal-title":"Structure"},{"key":"pcbi-0040043-b021","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1016\/j.jmb.2005.08.071","article-title":"Divergent evolution within protein superfolds inferred from profile-based phylogenetics.","volume":"354","year":"2005","journal-title":"J Mol Biol"},{"key":"pcbi-0040043-b022","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1038\/nature03199","article-title":"Simultaneous determination of protein structure and dynamics.","volume":"433","year":"2005","journal-title":"Nature"},{"key":"pcbi-0040043-b023","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","year":"2007","journal-title":"J Biomol NMR"},{"key":"pcbi-0040043-b024","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/S1359-0278(98)00035-2","article-title":"A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies.","volume":"3","year":"1998","journal-title":"Fold Des"},{"key":"pcbi-0040043-b025","doi-asserted-by":"crossref","first-page":"19545","DOI":"10.1016\/S0021-9258(19)36550-0","article-title":"Novel ubiquitin-like ribosomal protein fusion genes from the nematodes Caenorhabditis elegans and Caenorhabditis briggsae.","volume":"268","year":"1993","journal-title":"J Biol Chem"},{"key":"pcbi-0040043-b026","doi-asserted-by":"crossref","first-page":"5195","DOI":"10.1021\/bi0361620","article-title":"Exploring sequence\/folding space: Folding studies on multiple hydrophobic core mutants of ubiquitin.","volume":"43","year":"2004","journal-title":"Biochemistry"},{"key":"pcbi-0040043-b027","doi-asserted-by":"crossref","first-page":"1845","DOI":"10.1039\/b600829c","article-title":"Ubiquitin: A small protein folding paradigm.","volume":"4","year":"2006","journal-title":"Org Biomol Chem"},{"key":"pcbi-0040043-b028","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1111\/j.2517-6161.1991.tb01825.x","article-title":"Procrustes methods in the statistical analysis of shape.","volume":"53","year":"1991","journal-title":"J Roy Stat Soc B Met"},{"key":"pcbi-0040043-b029","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1007\/BF00890247","article-title":"Euclidean distance matrix analysis (EDMA)\u2014Estimation of mean form and mean form difference.","volume":"25","year":"1993","journal-title":"Math Geol"},{"key":"pcbi-0040043-b030","unstructured":"ArnoldSF 1981 The theory of linear models and multivariate analysis New York Wiley 475 p."},{"key":"pcbi-0040043-b031","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1080\/00949659908811970","article-title":"The MLE algorithm for the matrix normal distribution.","volume":"64","year":"1999","journal-title":"J Stat Comput Sim"},{"key":"pcbi-0040043-b032","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.2517-6161.1977.tb01600.x","article-title":"Maximum likelihood from incomplete data via the EM algorithm.","volume":"39","year":"1977","journal-title":"J Roy Stat Soc B Met"},{"key":"pcbi-0040043-b033","doi-asserted-by":"crossref","unstructured":"PawitanY 2001 In all likelihood: Statistical modeling and inference using likelihood Oxford (United Kingdom) Clarendon Press 528","DOI":"10.1093\/oso\/9780198507659.001.0001"},{"key":"pcbi-0040043-b034","doi-asserted-by":"crossref","first-page":"1279","DOI":"10.1002\/pro.5560011006","article-title":"On the multiple simultaneous superposition of molecular-structures by rigid body transformations.","volume":"1","year":"1992","journal-title":"Protein Sci"},{"key":"pcbi-0040043-b035","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1107\/S0108767387099215","article-title":"Superimposing several sets of atomic coordinates.","volume":"43","year":"1987","journal-title":"Acta Crystallogr A"},{"key":"pcbi-0040043-b036","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1002\/jcc.540111011","article-title":"An algorithm for the simultaneous superposition of a structural series.","volume":"11","year":"1990","journal-title":"J Comput Chem"},{"key":"pcbi-0040043-b037","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1107\/S010876739100867X","article-title":"A method for multiple superposition of structures.","volume":"48","year":"1992","journal-title":"Acta Crystallogr A"},{"key":"pcbi-0040043-b038","doi-asserted-by":"crossref","unstructured":"BournePEShindyalovIN 2003 Structure comparison and alignment. In: BournePEWeissigH Structural Bioinformatics Hoboken (New Jersey) Wiley-Liss 321 337","DOI":"10.1002\/0471721204.ch16"},{"key":"pcbi-0040043-b039","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank.","volume":"28","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040043-b040","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1038\/nsb1203-980","article-title":"Announcing the worldwide protein data bank.","volume":"10","year":"2003","journal-title":"Nat Struct Biol"},{"key":"pcbi-0040043-b041","unstructured":"DeLanoW 2002 The PyMOL Molecular Graphics System [computer program] Available: http:\/\/www.pymol.org\/. Accessed 18 January 2008."},{"key":"pcbi-0040043-b042","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/S0968-0004(00)89080-5","article-title":"RASMOL: Biomolecular graphics for all.","volume":"20","year":"1995","journal-title":"Trends Biochem Sci"},{"key":"pcbi-0040043-b043","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1107\/S0021889891004399","article-title":"MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures.","volume":"24","year":"1991","journal-title":"J App Cryst"},{"key":"pcbi-0040043-b044","doi-asserted-by":"crossref","first-page":"6996","DOI":"10.1093\/emboj\/16.23.6996","article-title":"Solution structure and basis for functional activity of stromal cell-derived factor-1; dissociation of cxcr4 activation from binding and inhibition of HIV-1.","volume":"16","year":"1997","journal-title":"EMBO J"},{"key":"pcbi-0040043-b045","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1107\/S0021889803006721","article-title":"POVScript+: A program for model and data visualization using persistence of vision ray-tracing.","volume":"36","year":"2003","journal-title":"J App Cryst"},{"key":"pcbi-0040043-b046","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1107\/S0907444994006396","article-title":"Raster3D Version 2.0: A program for photorealistic molecular graphics.","volume":"50","year":"1994","journal-title":"Acta Crystallogr D Biol Crystallogr"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0040043","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T10:48:24Z","timestamp":1737974904000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0040043"}},"subtitle":[],"editor":[{"given":"Roland","family":"Dunbrack","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2008,2,15]]},"references-count":46,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2008,2,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.0040043","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,2,15]]}}}