{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T22:31:08Z","timestamp":1781130668512,"version":"3.54.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,27]],"date-time":"2019-08-27T00:00:00Z","timestamp":1566864000000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012818","name":"Comunidad de Madrid","doi-asserted-by":"publisher","award":["S2017\/BMD-3817"],"award-info":[{"award-number":["S2017\/BMD-3817"]}],"id":[{"id":"10.13039\/100012818","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Spanish Ministry of Economy and Competitiveness","award":["BIO2016-76400-R"],"award-info":[{"award-number":["BIO2016-76400-R"]}]},{"name":"European Union and Horizon 2020","award":["INFRADEV-03-2016-2017"],"award-info":[{"award-number":["INFRADEV-03-2016-2017"]}]},{"name":"iNEXT","award":["INFRAIA-1-2014-2015"],"award-info":[{"award-number":["INFRAIA-1-2014-2015"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Recent technological advances and computational developments have allowed the reconstruction of Cryo-Electron Microscopy (cryo-EM) maps at near-atomic resolution. On a typical workflow and once the cryo-EM map has been calculated, a sharpening process is usually performed to enhance map visualization, a step that has proven very important in the key task of structural modeling. However, sharpening approaches, in general, neglects the local quality of the map, which is clearly suboptimal.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, a new method for local sharpening of cryo-EM density maps is proposed. The algorithm, named LocalDeblur, is based on a local resolution-guided Wiener restoration approach of the original map. The method is fully automatic and, from the user point of view, virtually parameter-free, without requiring either a starting model or introducing any additional structure factor correction or boosting. Results clearly show a significant impact on map interpretability, greatly helping modeling. In particular, this local sharpening approach is especially suitable for maps that present a broad resolution range, as is often the case for membrane proteins or macromolecules with high flexibility, all of them otherwise very suitable and interesting specimens for cryo-EM. To our knowledge, and leaving out the use of local filters, it represents the first application of local resolution in cryo-EM sharpening.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code (LocalDeblur) can be found at https:\/\/github.com\/I2PC\/xmipp and can be run using Scipion (http:\/\/scipion.cnb.csic.es) (release numbers greater than or equal 1.2.1).<\/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\/btz671","type":"journal-article","created":{"date-parts":[[2019,8,22]],"date-time":"2019-08-22T08:13:39Z","timestamp":1566461619000},"page":"765-772","source":"Crossref","is-referenced-by-count":142,"title":["Automatic local resolution-based sharpening of cryo-EM maps"],"prefix":"10.1093","volume":"36","author":[{"given":"Erney","family":"Ram\u00edrez-Aportela","sequence":"first","affiliation":[{"name":"Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Univ. Aut\u00f3noma de Madrid , Cantoblanco, 28049 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose Luis","family":"Vilas","sequence":"additional","affiliation":[{"name":"Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Univ. Aut\u00f3noma de Madrid , Cantoblanco, 28049 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alisa","family":"Glukhova","sequence":"additional","affiliation":[{"name":"Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences , Parkville, 3052 VIC, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberto","family":"Melero","sequence":"additional","affiliation":[{"name":"Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Univ. Aut\u00f3noma de Madrid , Cantoblanco, 28049 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pablo","family":"Conesa","sequence":"additional","affiliation":[{"name":"Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Univ. Aut\u00f3noma de Madrid , Cantoblanco, 28049 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marta","family":"Mart\u00ednez","sequence":"additional","affiliation":[{"name":"Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Univ. Aut\u00f3noma de Madrid , Cantoblanco, 28049 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Maluenda","sequence":"additional","affiliation":[{"name":"Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Univ. Aut\u00f3noma de Madrid , Cantoblanco, 28049 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Javier","family":"Mota","sequence":"additional","affiliation":[{"name":"Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Univ. Aut\u00f3noma de Madrid , Cantoblanco, 28049 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amaya","family":"Jim\u00e9nez","sequence":"additional","affiliation":[{"name":"Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Univ. Aut\u00f3noma de Madrid , Cantoblanco, 28049 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7519-6106","authenticated-orcid":false,"given":"Javier","family":"Vargas","sequence":"additional","affiliation":[{"name":"Department of Anatomy and Cell Biology, McGill University , 3640 Rue University, Montreal QC H3A 0C7 Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberto","family":"Marabini","sequence":"additional","affiliation":[{"name":"Campus Univ. Aut\u00f3noma de Madrid, Univ. Aut\u00f3noma de Madrid , 28049 Cantoblanco, Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick M","family":"Sexton","sequence":"additional","affiliation":[{"name":"Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences , Parkville, 3052 VIC, Australia"},{"name":"School of Pharmacy, Fudan University , Shanghai 201203, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose Maria","family":"Carazo","sequence":"additional","affiliation":[{"name":"Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Univ. Aut\u00f3noma de Madrid , Cantoblanco, 28049 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos Oscar S","family":"Sorzano","sequence":"additional","affiliation":[{"name":"Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Univ. Aut\u00f3noma de Madrid , Cantoblanco, 28049 Madrid, Spain"},{"name":"Campus Urb. Montepr\u00edncipe, Univ. CEU San Pablo , Boadilla del Monte, 28668 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,8,26]]},"reference":[{"key":"2023013110020560200_btz671-B1","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1107\/S0907444909052925","article-title":"PHENIX: a comprehensive Python-based system for macromolecular structure solution","volume":"66","author":"Adams","year":"2010","journal-title":"Acta Crystallogr. D Biol. Crystallogr"},{"key":"2023013110020560200_btz671-B2","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1107\/S2052252518001616","article-title":"X-ray and cryo-EM structures of inhibitor-bound cytochrome bc1 complexes for structure-based drug discovery","volume":"5","author":"Amporndanai","year":"2018","journal-title":"IUCrJ"},{"key":"2023013110020560200_btz671-B3","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1038\/nmeth.3541","article-title":"EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy","volume":"12","author":"Barad","year":"2015","journal-title":"Nat. Methods"},{"key":"2023013110020560200_btz671-B4","doi-asserted-by":"crossref","first-page":"1582","DOI":"10.1126\/science.1077945","article-title":"Crystal structure of Escherichia coli MscS, a voltage-modulated and mechanosensitive channel","volume":"298","author":"Bass","year":"2002","journal-title":"Science"},{"key":"2023013110020560200_btz671-B5","doi-asserted-by":"crossref","first-page":"e06380","DOI":"10.7554\/eLife.06380","article-title":"2.8 \u00c5 resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy","volume":"4","author":"Campbell","year":"2015","journal-title":"Elife"},{"key":"2023013110020560200_btz671-B6","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1016\/j.jsb.2013.08.002","article-title":"One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions","volume":"184","author":"Cardone","year":"2013","journal-title":"J. Struct. Biol"},{"key":"2023013110020560200_btz671-B7","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1107\/S0907444909042073","article-title":"MolProbity: all-atom structure validation for macromolecular crystallography","volume":"66","author":"Chen","year":"2010","journal-title":"Acta Crystallogr. D Biol. Crystallogr"},{"key":"2023013110020560200_btz671-B8","doi-asserted-by":"crossref","first-page":"e36497","DOI":"10.7554\/eLife.36497","article-title":"NSF-mediated disassembly of on- and off-pathway SNARE complexes and inhibition by complexin","volume":"7","author":"Choi","year":"2018","journal-title":"Elife"},{"key":"2023013110020560200_btz671-B9","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1021\/acsptsci.8b00056","article-title":"The molecular control of calcitonin receptor signaling","volume":"2","author":"Dal Maso","year":"2019","journal-title":"ACS Pharmacol. Transl. Sci"},{"key":"2023013110020560200_btz671-B10","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/j.jsb.2013.09.015","article-title":"Xmipp 3.0: an improved software suite for image processing in electron microscopy","volume":"184","author":"de la Rosa-Trevin","year":"2013","journal-title":"J. Struct. Biol"},{"key":"2023013110020560200_btz671-B11","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.jsb.2016.04.010","article-title":"Scipion: a software framework toward integration, reproducibility and validation in 3D electron microscopy","volume":"195","author":"de la Rosa-Trevin","year":"2016","journal-title":"J. Struct. Biol"},{"key":"2023013110020560200_btz671-B12","doi-asserted-by":"crossref","first-page":"2126","DOI":"10.1107\/S0907444904019158","article-title":"Coot: model-building tools for molecular graphics","volume":"60","author":"Emsley","year":"2004","journal-title":"Acta Crystallogr. D Biol. Crystallogr"},{"key":"2023013110020560200_btz671-B13","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/j.jsb.2018.08.010","article-title":"The first single particle analysis Map Challenge: a summary of the assessments","volume":"204","author":"Heymann","year":"2018","journal-title":"J. Struct. Biol"},{"key":"2023013110020560200_btz671-B14","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1038\/s41594-017-0011-7","article-title":"Structure and dynamics of GPCR signaling complexes","volume":"25","author":"Hilger","year":"2018","journal-title":"Nat. Struct. Mol. Biol"},{"key":"2023013110020560200_btz671-B15","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1107\/S0365110X61001893","article-title":"The crystal and molecular structure of cellobiose","volume":"14","author":"Jacobson","year":"1961","journal-title":"Acta Crystallogr"},{"key":"2023013110020560200_btz671-B16","doi-asserted-by":"crossref","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":"2023013110020560200_btz671-B17","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1038\/nmeth.2727","article-title":"Quantifying the local resolution of cryo-EM density maps","volume":"11","author":"Kucukelbir","year":"2014","journal-title":"Nat. Methods"},{"key":"2023013110020560200_btz671-B18","doi-asserted-by":"crossref","first-page":"D396","DOI":"10.1093\/nar\/gkv1126","article-title":"EMDataBank unified data resource for 3DEM","volume":"44","author":"Lawson","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023013110020560200_btz671-B19","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1038\/nature22327","article-title":"Phase-plate cryo-EM structure of a class B GPCR-G-protein complex","volume":"546","author":"Liang","year":"2017","journal-title":"Nature"},{"key":"2023013110020560200_btz671-B20","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1038\/s41586-018-0535-y","article-title":"Cryo-EM structure of the active, Gs-protein complexed, human CGRP receptor","volume":"561","author":"Liang","year":"2018","journal-title":"Nature"},{"key":"2023013110020560200_btz671-B21","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/nature12822","article-title":"Structure of the TRPV1 ion channel determined by electron cryo-microscopy","volume":"504","author":"Liao","year":"2013","journal-title":"Nature"},{"key":"2023013110020560200_btz671-B22","volume-title":"Information Theory, Inference, and Learning Algorithms","author":"Mackay","year":"2004"},{"key":"2023013110020560200_btz671-B23","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1107\/S0907444903025538","article-title":"On the interpretation and use of &lt;|E|2&gt;(d*) profiles","volume":"D60","author":"Morris","year":"2004","journal-title":"Acta Crystallogr. D Biol. Crystallogr"},{"key":"2023013110020560200_btz671-B24","doi-asserted-by":"crossref","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":"2023013110020560200_btz671-B25","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1016\/j.jmb.2003.07.013","article-title":"Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy","volume":"333","author":"Rosenthal","year":"2003","journal-title":"J. Mol. Biol"},{"key":"2023013110020560200_btz671-B26","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.jsb.2014.11.010","article-title":"Semi-automated selection of cryo-EM particles in RELION-1.3","volume":"189","author":"Scheres","year":"2015","journal-title":"J. Struct. Biol"},{"key":"2023013110020560200_btz671-B27","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.ultramic.2004.04.004","article-title":"Normalizing projection images: a study of image normalizing procedures for single particle three-dimensional electron microscopy","volume":"101","author":"Sorzano","year":"2004","journal-title":"Ultramicroscopy"},{"key":"2023013110020560200_btz671-B28","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1006\/jsbi.2001.4338","article-title":"The effect of overabundant projection directions on 3D reconstruction algorithms","volume":"133","author":"Sorzano","year":"2001","journal-title":"J. Struct. Biol"},{"key":"2023013110020560200_btz671-B29","doi-asserted-by":"crossref","first-page":"8","DOI":"10.3934\/biophy.2015.1.8","article-title":"Fast and accurate conversion of atomic models into electron density maps","volume":"2","author":"Sorzano","year":"2015","journal-title":"AIMS Biophys"},{"key":"2023013110020560200_btz671-B30","first-page":"6482567.","article-title":"A survey of the use of iterative reconstruction algorithms in electron microscopy","author":"Sorzano","year":"2017","journal-title":"Biomed. Res. Int., 2017"},{"key":"2023013110020560200_btz671-B31","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1107\/S2059798318004655","article-title":"Automated map sharpening by maximization of detail and connectivity","volume":"74","author":"Terwilliger","year":"2018","journal-title":"Acta Crystallogr. D Struct. Biol"},{"key":"2023013110020560200_btz671-B32","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.str.2017.12.018","article-title":"MonoRes: automatic and accurate estimation of local resolution for electron microscopy maps","volume":"26","author":"Vilas","year":"2018","journal-title":"Structure"},{"key":"2023013110020560200_btz671-B33","doi-asserted-by":"crossref","first-page":"e03080","DOI":"10.7554\/eLife.03080","article-title":"Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine","volume":"3","author":"Wong","year":"2014","journal-title":"Elife"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz671\/30040817\/btz671.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/3\/765\/48981612\/bioinformatics_36_3_765.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/3\/765\/48981612\/bioinformatics_36_3_765.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T13:49:12Z","timestamp":1675172952000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/3\/765\/5554698"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,8,26]]},"references-count":33,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2020,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz671","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/433284","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,2,1]]},"published":{"date-parts":[[2019,8,26]]}}}