{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T02:25:26Z","timestamp":1762050326236,"version":"3.41.2"},"reference-count":28,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,5,18]],"date-time":"2021-05-18T00:00:00Z","timestamp":1621296000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Mol. Biosci."],"abstract":"<jats:p>Significant technological developments and increasing scientific interest in cryogenic electron microscopy (cryo-EM) has resulted in a rapid increase in the amount of data generated by these experiments and the derived atomic models. Robust measures for the validation of 3D reconstructions and atomic models are essential for appropriate interpretation of the data. The resolution of data and availability of software tools that work across a range of resolutions often limit the quality of derived models. Hence, the final atomic model is often incomplete or contains regions where atomic positions are less reliable or incorrectly built. Extensive manual pruning and local adjustments or rebuilding are usually required to address these issues. The presented research introduces a software tool for the validation of the backbone trace of atomic models built in the cryo-EM density maps. In this study, we use the false discovery rate analysis, which can be used to segregate molecular signals from the background. Each atomic position in the model can be associated with an FDR backbone validation score, which can be used to identify potential mistraced residues. We demonstrate that the proposed validation score is complementary to existing validation metrics and is useful especially in cases where the model is built in the maps having varying local resolution. We also discuss the application of the score for automated pruning of atomic models built <jats:italic>ab-initio<\/jats:italic> during the iterative model building process in Buccaneer. We have implemented this score in the CCP-EM software suite.<\/jats:p>","DOI":"10.3389\/fmolb.2021.652530","type":"journal-article","created":{"date-parts":[[2021,5,18]],"date-time":"2021-05-18T04:22:31Z","timestamp":1621311751000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["Cryo-EM Map\u2013Based Model Validation Using the False Discovery Rate Approach"],"prefix":"10.3389","volume":"8","author":[{"given":"Mateusz","family":"Olek","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Agnel Praveen","family":"Joseph","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2021,5,18]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1107\/s2059798318009324","article-title":"New Tools for the Analysis and Validation of Cryo-EM Maps and Atomic Models","volume":"74","author":"Afonine","year":"2018","journal-title":"Acta Cryst. Sect D Struct. Biol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1038\/nature14892","article-title":"An Atomic Structure of Human \u03b3-Secretase","volume":"525","author":"Bai","year":"2015","journal-title":"Nature"},{"key":"B2","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1107\/s2052252518014434","article-title":"Thresholding of Cryo-EM Density Maps by False Discovery Rate Control","volume":"6","author":"Beckers","year":"2019","journal-title":"Int. Union Crystallogr. J."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.1214\/aos\/1013699998","article-title":"The Control of the False Discovery Rate in Multiple Testing under Dependency","volume":"29","author":"Benjamini","year":"2001","journal-title":"Ann. Stat."},{"key":"B4","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1107\/s2059798317007859","article-title":"Recent Developments in the CCP-EMsoftware Suite","volume":"73","author":"Burnley","year":"2017","journal-title":"Acta Cryst. Sect D Struct. Biol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1002","DOI":"10.1107\/s0907444906022116","article-title":"The Buccaneer Software for Automated Model Building. Acta Crystallogr. D 62","volume":"62","author":"Cowtan","year":"2006","journal-title":"Acta Crystallogr. Section D, Biol. Crystallogr."},{"key":"B6","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1107\/s0907444910007493","article-title":"Features and Development ofCoot","volume":"66","author":"Emsley","year":"2010","journal-title":"Acta Crystallogr. D Biol. Cryst."},{"key":"B7","doi-asserted-by":"publisher","first-page":"1032","DOI":"10.1038\/s41467-019-08991-8","article-title":"High-Resolution Structure Determination of Sub-100 KDa Complexes Using Conventional Cryo-EM","volume":"10","author":"Herzik","year":"2019","journal-title":"Nat. Commun."},{"key":"B8","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1107\/s2059798320005513","article-title":"Current Approaches for Automated Model Building into Cryo-EM Maps Using Buccaneer with CCP-EM","volume":"76","author":"Hoh","year":"2020","journal-title":"Acta Cryst. Sect D Struct. Biol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"e27131","DOI":"10.7554\/elife.27131","article-title":"Model-Based Local Density Sharpening of Cryo-EM Maps","volume":"6","author":"Jakobi","year":"2017","journal-title":"ELife"},{"key":"B10","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1016\/j.ymeth.2016.03.007","article-title":"Refinement of Atomic Models in High Resolution EM Reconstructions Using Flex-EM and Local Assessment","volume":"100","author":"Joseph","year":"2016","journal-title":"Methods"},{"key":"B11","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/j.jsb.2013.09.021","article-title":"Web-Based Visualisation and Analysis of 3D Electron-Microscopy Data from EMDB and PDB","volume":"184","author":"Lagerstedt","year":"2013","journal-title":"J. Struct. Biol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1016\/j.jsb.2018.10.004","article-title":"Comparing Cryo-EM Structures","volume":"204","author":"Lawson","year":"2018","journal-title":"J. Struct. Biol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1038\/s41592-020-01051-w","article-title":"Cryo-EM Model Validation Recommendations Based on Outcomes of the 2019 EMDataResource Challenge","volume":"18","author":"Lawson","year":"2021","journal-title":"Nat. Methods"},{"key":"B14","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1107\/s0907444911001314","article-title":"REFMAC5 for the Refinement of Macromolecular Crystal Structures","volume":"67","author":"Murshudov","year":"2011","journal-title":"Acta Crystallogr. Section D: Biol. Crystallogr."},{"key":"B15","unstructured":"Mrcfile: MRC File I\/O Library\n            PalmerC.\n          2016"},{"key":"B17","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera?A Visualization System for Exploratory Research and Analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2017525118","article-title":"DeepTracer for Fast De Novo Cryo-EM Protein Structure Modeling and Special Studies on CoV-Related Complexes","volume":"118","author":"Pfab","year":"2021","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B19","doi-asserted-by":"publisher","first-page":"2316","DOI":"10.1017\/s1431927620021170","article-title":"Measurement of Atom Resolvability in CryoEM Maps with Q-Scores","volume":"26","author":"Pintilie","year":"2020","journal-title":"Microsc. Microanal"},{"key":"B20","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1002\/pro.3786","article-title":"New Tools in MolProbity Validation: CaBLAM for CryoEM Backbone, UnDowser to Rethink \"waters,\" and NGL Viewer to Recapture Online 3D Graphics","volume":"29","author":"Prisant","year":"2020","journal-title":"Protein Sci."},{"key":"B21","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1038\/s41467-020-20295-w","article-title":"\u2018FSC-Q: A CryoEM Map-To-Atomic Model Quality Validation Based on the Local Fourier Shell Correlation\u2019","volume":"12","author":"Ram\u00edrez-Aportela","year":"2011","journal-title":"Nat. Commun."},{"key":"B22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1107\/s2052252519000277","article-title":"The Cryo-EM Revolution: Fueling the Next Phase","volume":"6","author":"Subramaniam","year":"2019","journal-title":"Int. Union Crystallogr. J."},{"key":"B23","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1002\/pro.3740","article-title":"Cryo\u2010EM Map Interpretation and Protein Model\u2010building Using Iterative Map Segmentation","volume":"29","author":"Terwilliger","year":"2020","journal-title":"Protein Sci."},{"key":"B24","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1002\/pro.3330","article-title":"MolProbity: More and Better Reference Data for Improved All-Atom Structure Validation","volume":"27","author":"Williams","year":"2018","journal-title":"Protein Sci."},{"key":"B25","unstructured":"Project-Gemmi\/Gemmi. C++. GEMMI\n            WojdyrM.\n          2017"},{"key":"B26","doi-asserted-by":"publisher","first-page":"1499","DOI":"10.1126\/science.abc1560","article-title":"Structural Basis for Inhibition of the RNA-dependent RNA Polymerase from SARS-CoV-2 by Remdesivir","volume":"368","author":"Yin","year":"2020","journal-title":"Science"},{"key":"B27","unstructured":"2019"},{"key":"B28","unstructured":"\u2018PyQt 4.9.4 Reference Guide\u20192011"}],"container-title":["Frontiers in Molecular Biosciences"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmolb.2021.652530\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,5,18]],"date-time":"2021-05-18T04:22:38Z","timestamp":1621311758000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmolb.2021.652530\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,18]]},"references-count":28,"alternative-id":["10.3389\/fmolb.2021.652530"],"URL":"https:\/\/doi.org\/10.3389\/fmolb.2021.652530","relation":{},"ISSN":["2296-889X"],"issn-type":[{"type":"electronic","value":"2296-889X"}],"subject":[],"published":{"date-parts":[[2021,5,18]]},"article-number":"652530"}}