{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,3,1]],"date-time":"2024-03-01T01:23:58Z","timestamp":1709256238319},"reference-count":34,"publisher":"Wiley","issue":"21","license":[{"start":{"date-parts":[[2021,5,14]],"date-time":"2021-05-14T00:00:00Z","timestamp":1620950400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100003074","name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica","doi-asserted-by":"publisher","award":["PICT\u201002212","PICT\u20100767"],"id":[{"id":"10.13039\/501100003074","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002923","name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","doi-asserted-by":"publisher","award":["PIP\u20100087"],"id":[{"id":"10.13039\/501100002923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[2021,8,5]]},"abstract":"Abstract<\/jats:title>We explore how ideas and practices common in Bayesian modeling can be applied to help assess the quality of 3D protein structural models. The basic premise of our approach is that the evaluation of a Bayesian statistical model's fit may reveal aspects of the quality of a structure when the fitted data is related to protein structural properties. Therefore, we fit a Bayesian hierarchical linear regression model to experimental and theoretical 13<\/jats:sup>C\u03b1<\/jats:italic><\/jats:sup> chemical shifts. Then, we propose two complementary approaches for the evaluation of such fitting: (a) in terms of the expected differences<\/jats:italic> between experimental and posterior predicted values; (b) in terms of the leave\u2010one\u2010out cross\u2010validation point\u2010wise predictive accuracy<\/jats:italic>. Finally, we present visualizations that can help interpret these evaluations. The analyses presented in this article are aimed to aid in detecting problematic residues in protein structures. The code developed for this work is available on: https:\/\/github.com\/BIOS-IMASL\/Hierarchical-Bayes-NMR-Validation<\/jats:ext-link>.<\/jats:p>","DOI":"10.1002\/jcc.26556","type":"journal-article","created":{"date-parts":[[2021,5,15]],"date-time":"2021-05-15T04:06:16Z","timestamp":1621051576000},"page":"1466-1474","update-policy":"http:\/\/dx.doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Exploring the quality of protein structural models from a Bayesian perspective"],"prefix":"10.1002","volume":"42","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-7249-755X","authenticated-orcid":false,"given":"Agustina","family":"Arroyuelo","sequence":"first","affiliation":[{"name":"Instituto de Matem\u00e1tica Aplicada San Luis CONICET\u2010UNSL San Luis Argentina"}]},{"given":"Jorge A.","family":"Vila","sequence":"additional","affiliation":[{"name":"Instituto de Matem\u00e1tica Aplicada San Luis CONICET\u2010UNSL San Luis Argentina"}]},{"given":"Osvaldo A.","family":"Martin","sequence":"additional","affiliation":[{"name":"Instituto de Matem\u00e1tica Aplicada San Luis CONICET\u2010UNSL San Luis Argentina"}]}],"member":"311","published-online":{"date-parts":[[2021,5,14]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja105832g"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-27225-7"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1371\/annotation\/2160e616-aa79-4097-96ab-e143d2a4d136"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.1501177"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.2253"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.9b10123"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2016.12.004"},{"key":"e_1_2_7_9_1","volume-title":"Bayesian Analysis with Python: Introduction to statistical modeling and probabilistic programming using PyMC3 and ArviZ","author":"Martin O.","year":"2018"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1201\/9780429029608"},{"key":"e_1_2_7_11_1","first-page":"1385","volume-title":"Advances in neural information processing systems","author":"Teh Y. W.","year":"2005"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1201\/b16018"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF00211777"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0908833106"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.861"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts179"},{"key":"e_1_2_7_17_1","unstructured":"A.Gelman A.Vehtari D.Simpson C. C.Margossian B.Carpenter Y.Yao L.Kennedy J.Gabry P.\u2010C.B\u00fcrkner andM.Modr\u00e1k Bayesian workflow arXiv:2011.01808 2020."},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11222-016-9696-4"},{"key":"e_1_2_7_19_1","unstructured":"A.Vehtari D.Simpson A.Gelman Y.Yao andJ.Gabry Pareto Smoothed Importance Sampling arXiv:1507.02646 2019."},{"key":"e_1_2_7_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.235"},{"key":"e_1_2_7_21_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10858-008-9221-y"},{"key":"e_1_2_7_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(87)90679-6"},{"key":"e_1_2_7_23_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja9812610"},{"key":"e_1_2_7_24_1","volume-title":"Doing Bayesian Data Analysis: A Tutorial with R, JAGS, and Stan","author":"Kruschke J.","year":"2014"},{"key":"e_1_2_7_25_1","first-page":"3571","volume":"11","author":"Watanabe S.","year":"2010","journal-title":"J. Mach. Learn. Res."},{"key":"e_1_2_7_26_1","doi-asserted-by":"publisher","DOI":"10.1111\/rssa.12378"},{"key":"e_1_2_7_27_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj-cs.55"},{"key":"e_1_2_7_28_1","doi-asserted-by":"publisher","DOI":"10.21105\/joss.01143"},{"key":"e_1_2_7_29_1","first-page":"82","volume-title":"CCP4 Newsletter on Protein Crystallography","author":"DeLano W. L.","year":"2002"},{"key":"e_1_2_7_30_1","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"e_1_2_7_31_1","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444909012086"},{"key":"e_1_2_7_32_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts179"},{"key":"e_1_2_7_33_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1315525110"},{"key":"e_1_2_7_34_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10858-011-9478-4"},{"key":"e_1_2_7_35_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10858-010-9433-9"}],"container-title":["Journal of Computational Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.26556","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/jcc.26556","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.26556","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,30]],"date-time":"2023-08-30T16:00:13Z","timestamp":1693411213000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.26556"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,14]]},"references-count":34,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2021,8,5]]}},"alternative-id":["10.1002\/jcc.26556"],"URL":"https:\/\/doi.org\/10.1002\/jcc.26556","archive":["Portico"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.07.27.223818","asserted-by":"object"}]},"ISSN":["0192-8651","1096-987X"],"issn-type":[{"value":"0192-8651","type":"print"},{"value":"1096-987X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,5,14]]},"assertion":[{"value":"2020-12-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-04-04","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-05-14","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}