{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T19:58:39Z","timestamp":1760731119865,"version":"3.37.3"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2018,9,4]],"date-time":"2018-09-04T00:00:00Z","timestamp":1536019200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["NSF-MCB-161759","NSF-CREST-1547848"],"award-info":[{"award-number":["NSF-MCB-161759","NSF-CREST-1547848"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["ERC-2012-AdG-323059"],"award-info":[{"award-number":["ERC-2012-AdG-323059"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Many proteins are partially disordered in physiological conditions and only fold, fully or partially, upon binding. Their structural analysis is challenging because the accessible information, typically chemical shifts (CS) from nuclear magnetic resonance experiments, are averages over broad ensembles of conformations. We aim to develop a database for the analysis of such data in terms of conformational distributions of the protein backbone rather than of individual high-resolution structures.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Glutton is the largest available database linking CS and protein 3D structures (5270 entries organized in three levels) and is searchable via a python script. It generates statistical distributions of \u03d5\u2212\u03c8 dihedral angles based on CS or vice versa. Such \u03d5\u2212\u03c8 distributions are used to calculate structural ensembles of partially disordered proteins from their CS. For folded proteins, such ensembles are excellent starting points for further refinement with additional experimental restraints (structure determination) or computational methods (structure prediction).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Glutton is freely available at https:\/\/github.com\/YeeHo\/Glutton.<\/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\/bty755","type":"journal-article","created":{"date-parts":[[2018,9,3]],"date-time":"2018-09-03T19:56:27Z","timestamp":1536004587000},"page":"1234-1236","source":"Crossref","is-referenced-by-count":4,"title":["Glutton: a tool for generating structural ensembles of partly disordered proteins from chemical shifts"],"prefix":"10.1093","volume":"35","author":[{"given":"Yi","family":"He","sequence":"first","affiliation":[{"name":"Department of Bioengineering, University of California Merced, Merced, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suhani","family":"Nagpal","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California Merced, Merced, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mourad","family":"Sadqi","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California Merced, Merced, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eva","family":"de Alba","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California Merced, Merced, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victor","family":"Mu\u00f1oz","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California Merced, Merced, CA, USA"},{"name":"IMDEA Nanoscience, Nanobiosystems Program, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,9,4]]},"reference":[{"key":"2023020108350031500_bty755-B1","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1042\/BST20160172","article-title":"The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease","volume":"44","author":"Babu","year":"2016","journal-title":"Biochem. Soc. Trans"},{"key":"2023020108350031500_bty755-B2","doi-asserted-by":"crossref","first-page":"4530","DOI":"10.1021\/jacs.6b00351","article-title":"Experimental inferential structure determination of ensembles for intrinsically disordered proteins","volume":"138","author":"Brookes","year":"2016","journal-title":"J. Am. Chem. Soc"},{"key":"2023020108350031500_bty755-B3","doi-asserted-by":"crossref","first-page":"16332","DOI":"10.1021\/ja904937a","article-title":"Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins","volume":"131","author":"De Simone","year":"2009","journal-title":"J. Am. Chem. Soc"},{"key":"2023020108350031500_bty755-B4","doi-asserted-by":"crossref","first-page":"3607","DOI":"10.1021\/cr030403s","article-title":"Unfolded proteins and protein folding studied by NMR","volume":"104","author":"Dyson","year":"2004","journal-title":"Chem. Rev"},{"key":"2023020108350031500_bty755-B5","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1021\/ac00200a003","article-title":"Protein structure determination in solution by two-dimensional and three-dimensional nuclear magnetic resonance spectroscopy","volume":"62","author":"Gronenborn","year":"1990","journal-title":"Anal. Chem"},{"key":"2023020108350031500_bty755-B6","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1002\/prot.21371","article-title":"From coarse-grain to all-atom: toward multiscale analysis of protein landscapes","volume":"68","author":"Heath","year":"2007","journal-title":"Proteins"},{"key":"2023020108350031500_bty755-B7","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1016\/j.sbi.2013.02.007","article-title":"Describing intrinsically disordered proteins at atomic resolution by NMR","volume":"23","author":"Jensen","year":"2013","journal-title":"Curr. Opin. Struct. Biol"},{"key":"2023020108350031500_bty755-B8","doi-asserted-by":"crossref","first-page":"12535","DOI":"10.1073\/pnas.1001693107","article-title":"Conformational selection in the molten globule state of the nuclear coactivator binding domain of CBP","volume":"107","author":"Kjaergaard","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020108350031500_bty755-B9","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1093\/bioinformatics\/bts701","article-title":"Characterization of disordered proteins with ENSEMBLE","volume":"29","author":"Krzeminski","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020108350031500_bty755-B10","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.sbi.2007.01.009","article-title":"Atomic-level characterization of disordered protein ensembles","volume":"17","author":"Mittag","year":"2007","journal-title":"Curr. Opin. Struct. Biol"},{"key":"2023020108350031500_bty755-B11","doi-asserted-by":"crossref","first-page":"12154","DOI":"10.1021\/ja204053n","article-title":"The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding","volume":"133","author":"Naganathan","year":"2011","journal-title":"J. Am. Chem. Soc"},{"key":"2023020108350031500_bty755-B12","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1093\/bioinformatics\/bts172","article-title":"Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables","volume":"28","author":"Ozenne","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020108350031500_bty755-B13","doi-asserted-by":"crossref","first-page":"L47","DOI":"10.1016\/j.bpj.2011.03.051","article-title":"How robust are protein folding simulations with respect to force field parameterization?","volume":"100","author":"Piana","year":"2011","journal-title":"Biophys. J"},{"key":"2023020108350031500_bty755-B14","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/s10858-010-9433-9","article-title":"SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network","volume":"48","author":"Shen","year":"2010","journal-title":"J. Biomol. NMR"},{"key":"2023020108350031500_bty755-B15","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1007\/s10858-013-9741-y","article-title":"Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks","volume":"56","author":"Shen","year":"2013","journal-title":"J. Biomol. NMR"},{"key":"2023020108350031500_bty755-B16","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1007\/s10858-009-9333-z","article-title":"TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts","volume":"44","author":"Shen","year":"2009","journal-title":"J. Biomol. NMR"},{"key":"2023020108350031500_bty755-B17","doi-asserted-by":"crossref","first-page":"e80","DOI":"10.7717\/peerj.80","article-title":"PeptideBuilder: a simple Python library to generate model peptides","volume":"1","author":"Tien","year":"2013","journal-title":"PeerJ"},{"key":"2023020108350031500_bty755-B18","doi-asserted-by":"crossref","first-page":"D402","DOI":"10.1093\/nar\/gkm957","article-title":"BioMagResBank","volume":"36","author":"Ulrich","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023020108350031500_bty755-B19","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1023\/A:1022836027055","article-title":"RefDB: a database of uniformly referenced protein chemical shifts","volume":"25","author":"Zhang","year":"2003","journal-title":"J. Biomol. NMR"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/7\/1234\/48968185\/bioinformatics_35_7_1234.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/7\/1234\/48968185\/bioinformatics_35_7_1234.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T19:40:38Z","timestamp":1675280438000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/7\/1234\/5090450"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,9,4]]},"references-count":19,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2019,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty755","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2019,4,1]]},"published":{"date-parts":[[2018,9,4]]}}}