{"id":"https://openalex.org/W7128915091","doi":"https://doi.org/10.5281/zenodo.17866461","title":"Gold-standard local validation enhances interpretability of cryo-EM maps","display_name":"Gold-standard local validation enhances interpretability of cryo-EM maps","publication_year":2025,"publication_date":"2025-12-09","ids":{"openalex":"https://openalex.org/W7128915091","doi":"https://doi.org/10.5281/zenodo.17866461"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.17866461","doi":"https://doi.org/10.5281/zenodo.17866461","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.17866461","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.17866461","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5124111727","display_name":"Javier Vargas","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I121748325","display_name":"Universidad Complutense de Madrid","ror":"https://ror.org/02p0gd045","country_code":"ES","type":"education","lineage":["https://openalex.org/I121748325"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Vargas, Javier","raw_affiliation_strings":["Universidad Complutense de Madrid"],"raw_orcid":"https://orcid.org/0000-0001-7519-6106","affiliations":[{"raw_affiliation_string":"Universidad Complutense de Madrid","institution_ids":["https://openalex.org/I121748325"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128579053","display_name":"Andreea V. Florea Toma","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I121748325","display_name":"Universidad Complutense de Madrid","ror":"https://ror.org/02p0gd045","country_code":"ES","type":"education","lineage":["https://openalex.org/I121748325"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Florea, Andreea V.","raw_affiliation_strings":["Universidad Complutense de Madrid"],"raw_orcid":"https://orcid.org/0009-0000-4475-9308","affiliations":[{"raw_affiliation_string":"Universidad Complutense de Madrid","institution_ids":["https://openalex.org/I121748325"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027541113","display_name":"Simone Pellegrino","orcid":"https://orcid.org/0000-0001-6302-2774","observed_orcids":["https://orcid.org/0000-0001-6302-2774"]},"institutions":[{"id":"https://openalex.org/I4210134489","display_name":"Bicycle Therapeutics (United Kingdom)","ror":"https://ror.org/03kq4dk33","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210134489"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Pellegrino, Simone","raw_affiliation_strings":["Bicycle Therapeutics (United Kingdom)"],"raw_orcid":"https://orcid.org/0000-0001-6302-2774","affiliations":[{"raw_affiliation_string":"Bicycle Therapeutics (United Kingdom)","institution_ids":["https://openalex.org/I4210134489"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004474408","display_name":"J. Burguet\u2013Castell","orcid":"https://orcid.org/0000-0002-9198-5380","observed_orcids":["https://orcid.org/0000-0002-9198-5380"]},"institutions":[{"id":"https://openalex.org/I88060688","display_name":"Universidad Polit\u00e9cnica de Madrid","ror":"https://ror.org/03n6nwv02","country_code":"ES","type":"education","lineage":["https://openalex.org/I88060688"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Burguet-Castell, Jordi","raw_affiliation_strings":["Universidad Polit\u00e9cnica de Madrid"],"raw_orcid":"https://orcid.org/0000-0002-9198-5380","affiliations":[{"raw_affiliation_string":"Universidad Polit\u00e9cnica de Madrid","institution_ids":["https://openalex.org/I88060688"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014240975","display_name":"Jose Antonio Gomez-Pedrero","orcid":"https://orcid.org/0000-0001-7043-3256","observed_orcids":["https://orcid.org/0000-0001-7043-3256"]},"institutions":[{"id":"https://openalex.org/I121748325","display_name":"Universidad Complutense de Madrid","ror":"https://ror.org/02p0gd045","country_code":"ES","type":"education","lineage":["https://openalex.org/I121748325"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"G\u00f3mez-Pedrero, Jose A","raw_affiliation_strings":["Universidad Complutense de Madrid"],"raw_orcid":"https://orcid.org/0000-0001-7043-3256","affiliations":[{"raw_affiliation_string":"Universidad Complutense de Madrid","institution_ids":["https://openalex.org/I121748325"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124691123","display_name":"Gustavo de Arruda Bezerra","orcid":"https://orcid.org/0000-0003-4471-821X","observed_orcids":["https://orcid.org/0000-0003-4471-821X"]},"institutions":[{"id":"https://openalex.org/I4210134489","display_name":"Bicycle Therapeutics (United Kingdom)","ror":"https://ror.org/03kq4dk33","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210134489"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Arruda Bezerra, Gustavo","raw_affiliation_strings":["Bicycle Therapeutics (United Kingdom)"],"raw_orcid":"https://orcid.org/0000-0003-4471-821X","affiliations":[{"raw_affiliation_string":"Bicycle Therapeutics (United Kingdom)","institution_ids":["https://openalex.org/I4210134489"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047143588","display_name":"Khanh Huy Bui","orcid":"https://orcid.org/0000-0003-2814-9889","observed_orcids":["https://orcid.org/0000-0003-2814-9889","https://orcid.org/0000-0001-8231-3016"]},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Bui, Khanh Huy","raw_affiliation_strings":["McGill University"],"raw_orcid":"https://orcid.org/0000-0003-2814-9889","affiliations":[{"raw_affiliation_string":"McGill University","institution_ids":["https://openalex.org/I5023651"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/figure-of-merit","display_name":"figure of merit","score":0.7720000147819519},{"id":"https://openalex.org/keywords/signal-to-noise-ratio-estimation","display_name":"signal-to-noise ratio estimation","score":0.9390000104904175},{"id":"https://openalex.org/keywords/local-anisotropy","display_name":"local anisotropy","score":0.875},{"id":"https://openalex.org/keywords/phase-information","display_name":"phase information","score":0.5320000052452087}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.9261000156402588},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6536999940872192},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.569100022315979},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.5336999893188477},{"id":"https://openalex.org/C2781137444","wikidata":"https://www.wikidata.org/wiki/Q237105","display_name":"Sharpening","level":2,"score":0.5315999984741211},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5293999910354614},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45820000767707825},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.38199999928474426},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3691999912261963},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.358599990606308},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34060001373291016},{"id":"https://openalex.org/C54170458","wikidata":"https://www.wikidata.org/wiki/Q663554","display_name":"Voxel","level":2,"score":0.33719998598098755},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.29269999265670776},{"id":"https://openalex.org/C104267543","wikidata":"https://www.wikidata.org/wiki/Q208163","display_name":"Signal processing","level":3,"score":0.27399998903274536},{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.2635999917984009},{"id":"https://openalex.org/C44280652","wikidata":"https://www.wikidata.org/wiki/Q104837","display_name":"Phase (matter)","level":2,"score":0.26170000433921814},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.26089999079704285},{"id":"https://openalex.org/C110384440","wikidata":"https://www.wikidata.org/wiki/Q1143270","display_name":"Upsampling","level":3,"score":0.2565000057220459},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.25}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.5281/zenodo.17866461","doi":"https://doi.org/10.5281/zenodo.17866461","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.17866461","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},{"id":"doi:10.5281/zenodo.17866462","doi":"https://doi.org/10.5281/zenodo.17866462","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.17866462","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},{"id":"doi:10.5281/zenodo.18878039","doi":"https://doi.org/10.5281/zenodo.18878039","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.18878039","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},{"id":"doi:10.5281/zenodo.20730619","doi":"https://doi.org/10.5281/zenodo.20730619","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.20730619","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.5281/zenodo.17866461","doi":"https://doi.org/10.5281/zenodo.17866461","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.17866461","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2576821842","display_name":null,"funder_award_id":"PID2022-137548OB-I00","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":"https://ror.org/003x0zc53"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3116396461","https://openalex.org/W3208440095","https://openalex.org/W2970462530","https://openalex.org/W4211010919","https://openalex.org/W2086812659","https://openalex.org/W7008966955","https://openalex.org/W2974844924","https://openalex.org/W3187187724","https://openalex.org/W4226337027","https://openalex.org/W4414190323"],"abstract_inverted_index":{"Accurate":[0],"interpretation":[1],"of":[2,11,57],"cryo-electron":[3],"microscopy":[4],"(cryo-EM)":[5],"maps":[6,75,136],"requires":[7],"robust":[8,160],"local":[9,53,92,98,114,120,161],"measures":[10],"quality":[12,107],"and":[13,29,31,55,68,76,105,111,118,130,143,163],"resolution.":[14],"Current":[15],"approaches":[16,126],"are":[17,81],"often":[18],"limited":[19],"by":[20,64],"single-map":[21],"estimates,":[22],"user-defined":[23],"solvent":[24],"masks":[25],"that":[26,60],"risk":[27],"bias":[28],"overfitting,":[30],"an":[32],"exclusive":[33],"reliance":[34],"on":[35],"signal":[36],"amplitudes":[37,67],"while":[38],"neglecting":[39],"phase":[40],"information.":[41],"Here,":[42],"we":[43],"present":[44],"a":[45,128],"Gold-standard":[46,119],"framework":[47],"requiring":[48],"minimal":[49],"user":[50],"intervention":[51],"for":[52,133,148],"validation":[54],"enhancement":[56],"cryo-EM":[58,135],"reconstructions":[59],"addresses":[61],"these":[62,125],"limitations":[63],"jointly":[65],"analyzing":[66],"phases":[69],"between":[70,74],"independent":[71,88],"half-maps":[72],"or":[73],"atomic":[77,149],"models.":[78],"All":[79],"methods":[80],"computed":[82],"voxel-wise":[83],"in":[84],"real":[85],"space":[86],"from":[87],"half-maps,":[89],"ensuring":[90],"unbiased":[91,97],"evaluation.":[93],"The":[94],"toolbox":[95],"includes":[96],"sharpening":[99],"(LocSpiral2),":[100],"per-voxel":[101],"figure-of-merit,":[102],"signal-to-noise":[103],"estimation":[104],"general":[106],"assessment":[108],"(LocFOM,":[109],"LocSNR":[110],"LocQ),":[112],"directional":[113],"anisotropy":[115],"evaluation":[116],"(LocAnisotropy)":[117],"resolution":[121],"mapping":[122],"(LocResMap).":[123],"Together,":[124],"provide":[127],"comprehensive":[129],"unified":[131],"strategy":[132],"evaluating":[134],"at":[137],"the":[138],"voxel":[139],"level,":[140],"improving":[141],"interpretability":[142],"offering":[144],"more":[145],"reliable":[146],"guidance":[147],"modelling.":[150],"Applications":[151],"to":[152],"challenging":[153],"experimental":[154],"datasets":[155],"demonstrate":[156],"enhanced":[157],"map":[158],"sharpening,":[159],"validation,":[162],"improved":[164],"structural":[165],"insights.":[166]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-02-15T00:00:00"}