{"id":"https://openalex.org/W7163362878","doi":"https://doi.org/10.1093/bioinformatics/btag350","title":"Benchmarking deep learning methods for C <i>\u03b1</i> atom prediction in cryo-EM density maps","display_name":"Benchmarking deep learning methods for C <i>\u03b1</i> atom prediction in cryo-EM density maps","publication_year":2026,"publication_date":"2026-05-27","ids":{"openalex":"https://openalex.org/W7163362878","doi":"https://doi.org/10.1093/bioinformatics/btag350","pmid":"https://pubmed.ncbi.nlm.nih.gov/42234518"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag350","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag350","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101679477","display_name":"Tian Zhang","orcid":"https://orcid.org/0000-0003-3054-3439"},"institutions":[{"id":"https://openalex.org/I108688024","display_name":"Qingdao University","ror":"https://ror.org/021cj6z65","country_code":"CN","type":"education","lineage":["https://openalex.org/I108688024"]},{"id":"https://openalex.org/I4210116869","display_name":"Affiliated Hospital of Qingdao University","ror":"https://ror.org/026e9yy16","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210116869"]},{"id":"https://openalex.org/I4210127460","display_name":"Ningxia Medical University","ror":"https://ror.org/02h8a1848","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210127460"]},{"id":"https://openalex.org/I4210161528","display_name":"Qilu Hospital of Shandong University","ror":"https://ror.org/056ef9489","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161528"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tian Zhang","raw_affiliation_strings":["College of Medical Information and Engineering, Ningxia Medical University , Yinchuan 750004,","Research Center for Mathematics and Interdisciplinary Sciences; Cheeloo College of Medicine, Qilu Hospital (Qingdao), Shandong University , Qingdao 266237,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Medical Information and Engineering, Ningxia Medical University , Yinchuan 750004,","institution_ids":["https://openalex.org/I4210127460"]},{"raw_affiliation_string":"Research Center for Mathematics and Interdisciplinary Sciences; Cheeloo College of Medicine, Qilu Hospital (Qingdao), Shandong University , Qingdao 266237,","institution_ids":["https://openalex.org/I4210116869","https://openalex.org/I108688024","https://openalex.org/I4210161528"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082256207","display_name":"Z Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I108688024","display_name":"Qingdao University","ror":"https://ror.org/021cj6z65","country_code":"CN","type":"education","lineage":["https://openalex.org/I108688024"]},{"id":"https://openalex.org/I4210116869","display_name":"Affiliated Hospital of Qingdao University","ror":"https://ror.org/026e9yy16","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210116869"]},{"id":"https://openalex.org/I4210127460","display_name":"Ningxia Medical University","ror":"https://ror.org/02h8a1848","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210127460"]},{"id":"https://openalex.org/I4210161528","display_name":"Qilu Hospital of Shandong University","ror":"https://ror.org/056ef9489","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161528"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhe Liu","raw_affiliation_strings":["College of Medical Information and Engineering, Ningxia Medical University , Yinchuan 750004,","Research Center for Mathematics and Interdisciplinary Sciences; Cheeloo College of Medicine, Qilu Hospital (Qingdao), Shandong University , Qingdao 266237,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Medical Information and Engineering, Ningxia Medical University , Yinchuan 750004,","institution_ids":["https://openalex.org/I4210127460"]},{"raw_affiliation_string":"Research Center for Mathematics and Interdisciplinary Sciences; Cheeloo College of Medicine, Qilu Hospital (Qingdao), Shandong University , Qingdao 266237,","institution_ids":["https://openalex.org/I4210116869","https://openalex.org/I108688024","https://openalex.org/I4210161528"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085228291","display_name":"Yiqing Ma","orcid":"https://orcid.org/0000-0001-5139-8643"},"institutions":[{"id":"https://openalex.org/I108688024","display_name":"Qingdao University","ror":"https://ror.org/021cj6z65","country_code":"CN","type":"education","lineage":["https://openalex.org/I108688024"]},{"id":"https://openalex.org/I4210116869","display_name":"Affiliated Hospital of Qingdao University","ror":"https://ror.org/026e9yy16","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210116869"]},{"id":"https://openalex.org/I4210127460","display_name":"Ningxia Medical University","ror":"https://ror.org/02h8a1848","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210127460"]},{"id":"https://openalex.org/I4210161528","display_name":"Qilu Hospital of Shandong University","ror":"https://ror.org/056ef9489","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161528"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yiqing Ma","raw_affiliation_strings":["College of Medical Information and Engineering, Ningxia Medical University , Yinchuan 750004,","Research Center for Mathematics and Interdisciplinary Sciences; Cheeloo College of Medicine, Qilu Hospital (Qingdao), Shandong University , Qingdao 266237,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Medical Information and Engineering, Ningxia Medical University , Yinchuan 750004,","institution_ids":["https://openalex.org/I4210127460"]},{"raw_affiliation_string":"Research Center for Mathematics and Interdisciplinary Sciences; Cheeloo College of Medicine, Qilu Hospital (Qingdao), Shandong University , Qingdao 266237,","institution_ids":["https://openalex.org/I4210116869","https://openalex.org/I108688024","https://openalex.org/I4210161528"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068167694","display_name":"Chenjie Feng","orcid":"https://orcid.org/0000-0001-7898-9291"},"institutions":[{"id":"https://openalex.org/I4210127460","display_name":"Ningxia Medical University","ror":"https://ror.org/02h8a1848","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210127460"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chenjie Feng","raw_affiliation_strings":["College of Medical Information and Engineering, Ningxia Medical University , Yinchuan 750004,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Medical Information and Engineering, Ningxia Medical University , Yinchuan 750004,","institution_ids":["https://openalex.org/I4210127460"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5137779599","display_name":"Renmin Han","orcid":null},"institutions":[{"id":"https://openalex.org/I108688024","display_name":"Qingdao University","ror":"https://ror.org/021cj6z65","country_code":"CN","type":"education","lineage":["https://openalex.org/I108688024"]},{"id":"https://openalex.org/I4210116869","display_name":"Affiliated Hospital of Qingdao University","ror":"https://ror.org/026e9yy16","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210116869"]},{"id":"https://openalex.org/I4210161528","display_name":"Qilu Hospital of Shandong University","ror":"https://ror.org/056ef9489","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161528"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Renmin Han","raw_affiliation_strings":["Research Center for Mathematics and Interdisciplinary Sciences; Cheeloo College of Medicine, Qilu Hospital (Qingdao), Shandong University , Qingdao 266237,"],"raw_orcid":"https://orcid.org/0000-0003-4761-6526","affiliations":[{"raw_affiliation_string":"Research Center for Mathematics and Interdisciplinary Sciences; Cheeloo College of Medicine, Qilu Hospital (Qingdao), Shandong University , Qingdao 266237,","institution_ids":["https://openalex.org/I4210116869","https://openalex.org/I108688024","https://openalex.org/I4210161528"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5068167694","https://openalex.org/A5137779599"],"corresponding_institution_ids":["https://openalex.org/I108688024","https://openalex.org/I4210116869","https://openalex.org/I4210127460","https://openalex.org/I4210161528"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.79641186,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"6","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":0.8353000283241272,"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":0.8353000283241272,"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":0.07519999891519547,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.0364999994635582,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.8549000024795532},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.8500000238418579},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.5939000248908997},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5597000122070312},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5478000044822693},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5418999791145325},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.5049999952316284},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.5041000247001648}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.8549000024795532},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.8500000238418579},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7444000244140625},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6532999873161316},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.5939000248908997},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5597000122070312},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5478000044822693},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5418999791145325},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5358999967575073},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5343000292778015},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.5049999952316284},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.5041000247001648},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4408999979496002},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.42890000343322754},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.42340001463890076},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.4221000075340271},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4027999937534332},{"id":"https://openalex.org/C55037315","wikidata":"https://www.wikidata.org/wiki/Q5421151","display_name":"Experimental data","level":2,"score":0.34619998931884766},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3375999927520752},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.31040000915527344},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.26669999957084656},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.257099986076355},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.25099998712539673},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.250900000333786}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag350","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42234518","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42234518","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:13264388","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13264388/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag350","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1075678864","display_name":null,"funder_award_id":"32241027","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1321659228","display_name":null,"funder_award_id":"2021YFF0704300","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G1886166076","display_name":null,"funder_award_id":"624B2089","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5594712245","display_name":null,"funder_award_id":"12501589","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7516056161","display_name":null,"funder_award_id":"W2511070","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7667897608","display_name":null,"funder_award_id":"62472034","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1520649887","https://openalex.org/W1901129140","https://openalex.org/W1983952778","https://openalex.org/W2028440694","https://openalex.org/W2051925784","https://openalex.org/W2072404529","https://openalex.org/W2397429809","https://openalex.org/W2621042378","https://openalex.org/W2791652956","https://openalex.org/W2802061004","https://openalex.org/W2912476242","https://openalex.org/W2928165649","https://openalex.org/W3005016287","https://openalex.org/W3010499032","https://openalex.org/W3015788359","https://openalex.org/W3209492740","https://openalex.org/W4309631284","https://openalex.org/W4313890332","https://openalex.org/W4387451605","https://openalex.org/W4389480950","https://openalex.org/W4392155415","https://openalex.org/W4400201692","https://openalex.org/W4403318777","https://openalex.org/W4416199605"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"With":[1],"the":[2,9,60,133,217],"advancement":[3],"of":[4,64,87,169],"cryo-electron":[5],"microscopy":[6],"(cryo-EM)":[7],"into":[8],"atomic":[10],"resolution":[11,153],"era,":[12],"accurate":[13],"C\u03b1":[14,41,61],"atom":[15],"modeling":[16,46],"has":[17],"become":[18],"essential":[19],"for":[20,39,118,216],"macromolecular":[21],"structure":[22,211],"determination.":[23,212],"However,":[24],"existing":[25],"evaluation":[26,98,135,201,220],"systems":[27],"overly":[28],"rely":[29],"on":[30,132],"full-atom":[31],"metrics":[32,105,221],"and":[33,73,93,120,137,207,219],"lack":[34],"a":[35,55,80,84,166,188,198],"dedicated,":[36],"comprehensive":[37],"benchmark":[38,57,218],"assessing":[40],"prediction":[42,62],"modules":[43],"within":[44],"automated":[45,209],"tools.":[47],"RESULTS:":[48],"To":[49],"address":[50],"this":[51],"gap,":[52],"we":[53],"establish":[54],"rigorous":[56],"to":[58,152,165,203],"evaluate":[59],"performance":[63,128],"four":[65],"prominent":[66],"deep":[67],"learning-based":[68],"methods":[69],"(ModelAngelo,":[70],"DeepMainMast,":[71],"EModelX,":[72],"CryoAtom)":[74],"across":[75,175],"multiple":[76],"dimensions.":[77],"We":[78],"construct":[79],"diverse":[81],"dataset":[82],"covering":[83],"wide":[85],"range":[86],"resolutions":[88],"(1-8":[89],"\u00c5),":[90],"molecular":[91],"weights,":[92],"noise":[94],"levels.":[95],"A":[96],"novel":[97],"framework":[99,202],"is":[100,129,222],"introduced,":[101],"incorporating":[102],"multi-threshold":[103],"RMSD-based":[104],"(1-3":[106],"\u00c5)":[107],"alongside":[108],"advanced":[109],"point-cloud":[110],"similarity":[111],"measures":[112],"(Chamfer":[113],"Distance,":[114],"Earth":[115],"Mover's":[116],"Distance)":[117],"quantitative":[119],"nuanced":[121],"assessment.":[122],"Our":[123],"results":[124],"reveal":[125],"that":[126],"method":[127,205],"highly":[130],"dependent":[131],"chosen":[134],"criteria":[136,185],"intrinsic":[138],"data":[139,148],"characteristics.":[140],"ModelAngelo":[141],"excels":[142],"under":[143,183],"loose":[144],"thresholds":[145],"with":[146],"high-quality":[147],"but":[149,186],"shows":[150],"sensitivity":[151],"degradation;":[154],"CryoAtom":[155],"demonstrates":[156,172],"notable":[157],"computational":[158,190],"efficiency,":[159],"however,":[160],"its":[161],"completeness-oriented":[162],"design":[163],"leads":[164],"certain":[167],"loss":[168],"precision;":[170],"EModelX":[171],"balanced":[173],"generalization":[174],"varied":[176],"conditions;":[177],"DeepMainMast":[178],"achieves":[179],"high":[180,189],"localization":[181],"accuracy":[182],"stringent":[184],"incurs":[187],"cost.":[191],"AVAILABILITY":[192],"AND":[193],"IMPLEMENTATION:":[194],"This":[195],"work":[196],"provides":[197],"reproducible,":[199],"C\u03b1-centric":[200],"guide":[204],"development":[206],"advance":[208],"cryo-EM":[210],"The":[213],"source":[214],"code":[215],"freely":[223],"available":[224],"at":[225],"https://github.com/zhtianz/Benchmarking\\_CA.":[226]},"counts_by_year":[],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2026-06-04T00:00:00"}