{"id":"https://openalex.org/W4282917556","doi":"https://doi.org/10.1021/acs.jcim.2c00522","title":"Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network","display_name":"Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network","publication_year":2022,"publication_date":"2022-06-09","ids":{"openalex":"https://openalex.org/W4282917556","doi":"https://doi.org/10.1021/acs.jcim.2c00522","pmid":"https://pubmed.ncbi.nlm.nih.gov/35679182"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c00522","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00522","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.2c00522","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038390928","display_name":"Vincenzo Laveglia","orcid":"https://orcid.org/0000-0002-2358-7268"},"institutions":[{"id":"https://openalex.org/I4210144939","display_name":"Interuniversity Consortium for Magnetic Resonance","ror":"https://ror.org/04v403p80","country_code":"IT","type":"education","lineage":["https://openalex.org/I4210144939"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Vincenzo Laveglia","raw_affiliation_strings":["Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049779098","display_name":"Andrea Giachetti","orcid":"https://orcid.org/0000-0002-2722-566X"},"institutions":[{"id":"https://openalex.org/I4210144939","display_name":"Interuniversity Consortium for Magnetic Resonance","ror":"https://ror.org/04v403p80","country_code":"IT","type":"education","lineage":["https://openalex.org/I4210144939"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Giachetti","raw_affiliation_strings":["Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037621960","display_name":"Davide Sala","orcid":"https://orcid.org/0000-0002-3900-0011"},"institutions":[{"id":"https://openalex.org/I4210144939","display_name":"Interuniversity Consortium for Magnetic Resonance","ror":"https://ror.org/04v403p80","country_code":"IT","type":"education","lineage":["https://openalex.org/I4210144939"]},{"id":"https://openalex.org/I45084792","display_name":"University of Florence","ror":"https://ror.org/04jr1s763","country_code":"IT","type":"education","lineage":["https://openalex.org/I45084792"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE","IT"],"is_corresponding":false,"raw_author_name":"Davide Sala","raw_affiliation_strings":["Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy","Institute for Drug Discovery, Leipzig University, Br\u00fcderstr. 34, 04103 Leipzig, Germany","Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy"],"raw_orcid":"https://orcid.org/0000-0002-3900-0011","affiliations":[{"raw_affiliation_string":"Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939"]},{"raw_affiliation_string":"Institute for Drug Discovery, Leipzig University, Br\u00fcderstr. 34, 04103 Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079457434","display_name":"Claudia Andreini","orcid":"https://orcid.org/0000-0003-4329-8225"},"institutions":[{"id":"https://openalex.org/I4210144939","display_name":"Interuniversity Consortium for Magnetic Resonance","ror":"https://ror.org/04v403p80","country_code":"IT","type":"education","lineage":["https://openalex.org/I4210144939"]},{"id":"https://openalex.org/I45084792","display_name":"University of Florence","ror":"https://ror.org/04jr1s763","country_code":"IT","type":"education","lineage":["https://openalex.org/I45084792"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Claudia Andreini","raw_affiliation_strings":["Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy","Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939"]},{"raw_affiliation_string":"Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I45084792"]},{"raw_affiliation_string":"Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084306542","display_name":"Antonio Rosato","orcid":"https://orcid.org/0000-0001-6172-0368"},"institutions":[{"id":"https://openalex.org/I4210144939","display_name":"Interuniversity Consortium for Magnetic Resonance","ror":"https://ror.org/04v403p80","country_code":"IT","type":"education","lineage":["https://openalex.org/I4210144939"]},{"id":"https://openalex.org/I45084792","display_name":"University of Florence","ror":"https://ror.org/04jr1s763","country_code":"IT","type":"education","lineage":["https://openalex.org/I45084792"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Antonio Rosato","raw_affiliation_strings":["Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy","Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy"],"raw_orcid":"https://orcid.org/0000-0001-6172-0368","affiliations":[{"raw_affiliation_string":"Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939"]},{"raw_affiliation_string":"Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I45084792"]},{"raw_affiliation_string":"Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5079457434","https://openalex.org/A5084306542"],"corresponding_institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"],"apc_list":null,"apc_paid":null,"fwci":1.3019,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.79223242,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"62","issue":"12","first_page":"2951","last_page":"2960"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9988999962806702,"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"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9988999962806702,"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"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9987000226974487,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9983999729156494,"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/classifier","display_name":"Classifier (UML)","score":0.6208317279815674},{"id":"https://openalex.org/keywords/metalloprotein","display_name":"Metalloprotein","score":0.5421285629272461},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4910399913787842},{"id":"https://openalex.org/keywords/metal","display_name":"Metal","score":0.45592501759529114},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.44977495074272156},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.4456188380718231},{"id":"https://openalex.org/keywords/zinc","display_name":"Zinc","score":0.41786059737205505},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3902280330657959},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.32586026191711426},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.323982834815979},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.28848588466644287},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23265627026557922},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.20634031295776367}],"concepts":[{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.6208317279815674},{"id":"https://openalex.org/C17165728","wikidata":"https://www.wikidata.org/wiki/Q423350","display_name":"Metalloprotein","level":3,"score":0.5421285629272461},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4910399913787842},{"id":"https://openalex.org/C544153396","wikidata":"https://www.wikidata.org/wiki/Q11426","display_name":"Metal","level":2,"score":0.45592501759529114},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.44977495074272156},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.4456188380718231},{"id":"https://openalex.org/C535196362","wikidata":"https://www.wikidata.org/wiki/Q758","display_name":"Zinc","level":2,"score":0.41786059737205505},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3902280330657959},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.32586026191711426},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.323982834815979},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.28848588466644287},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23265627026557922},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.20634031295776367},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008670","descriptor_name":"Metals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008670","descriptor_name":"Metals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008670","descriptor_name":"Metals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.2c00522","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00522","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:35679182","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35679182","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":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:flore.unifi.it:2158/1285440","is_oa":true,"landing_page_url":"https://pubs.acs.org/doi/10.1021/acs.jcim.2c00522","pdf_url":null,"source":{"id":"https://openalex.org/S4306402033","display_name":"Florence Research (University of Florence)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45084792","host_organization_name":"University of Florence","host_organization_lineage":["https://openalex.org/I45084792"],"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":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9241070","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9241070","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":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.2c00522","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00522","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6200000047683716,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G2687563341","display_name":null,"funder_award_id":"824087","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5588463944","display_name":null,"funder_award_id":"101017567","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1498436455","https://openalex.org/W1800266928","https://openalex.org/W1801288333","https://openalex.org/W1982003073","https://openalex.org/W1986171863","https://openalex.org/W1995808589","https://openalex.org/W1998230257","https://openalex.org/W2018285957","https://openalex.org/W2029263948","https://openalex.org/W2051210555","https://openalex.org/W2073798474","https://openalex.org/W2082439356","https://openalex.org/W2086004174","https://openalex.org/W2109553965","https://openalex.org/W2110485445","https://openalex.org/W2112796928","https://openalex.org/W2113723577","https://openalex.org/W2127637467","https://openalex.org/W2145661853","https://openalex.org/W2146788987","https://openalex.org/W2147431408","https://openalex.org/W2148386309","https://openalex.org/W2151687360","https://openalex.org/W2157331557","https://openalex.org/W2158698691","https://openalex.org/W2520301867","https://openalex.org/W2544136853","https://openalex.org/W2557595285","https://openalex.org/W2583454016","https://openalex.org/W2589875042","https://openalex.org/W2598400083","https://openalex.org/W2767581071","https://openalex.org/W2783510959","https://openalex.org/W2787894218","https://openalex.org/W2800057751","https://openalex.org/W2895930884","https://openalex.org/W2912446381","https://openalex.org/W2914874661","https://openalex.org/W2919115771","https://openalex.org/W2922912766","https://openalex.org/W2936951059","https://openalex.org/W2962772482","https://openalex.org/W2970764100","https://openalex.org/W2972411752","https://openalex.org/W2987090428","https://openalex.org/W2991957026","https://openalex.org/W2997492748","https://openalex.org/W3093816012","https://openalex.org/W3116548791","https://openalex.org/W3169686454","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3199548378","https://openalex.org/W4231059664","https://openalex.org/W4234165528","https://openalex.org/W4298869505","https://openalex.org/W4388245583"],"related_works":["https://openalex.org/W3126783617","https://openalex.org/W3093468851","https://openalex.org/W4280624450","https://openalex.org/W2121688928","https://openalex.org/W2732388178","https://openalex.org/W2185518315","https://openalex.org/W2806488847","https://openalex.org/W4353055924","https://openalex.org/W1495233806","https://openalex.org/W1483608757"],"abstract_inverted_index":{"Thirty-eight":[0],"percent":[1],"of":[2,41,73,99,111,119,138,155,171,188,199,201,221,237,241],"protein":[3,246],"structures":[4,72],"in":[5,33,48,69,190,206,245],"the":[6,34,39,70,77,85,94,108,124,135,139,142,147,153,156,172,178,191,207,212,225,235,238],"Protein":[7],"Data":[8],"Bank":[9],"contain":[10],"at":[11],"least":[12],"one":[13,229],"metal":[14,20,179,182,192],"ion.":[15],"However,":[16],"not":[17,46],"all":[18],"these":[19],"sites":[21,68,82,115,129,145,165,244],"are":[22],"biologically":[23],"relevant.":[24],"Cations":[25],"present":[26,166],"as":[27],"impurities":[28],"during":[29],"sample":[30],"preparation":[31],"or":[32,230],"crystallization":[35],"buffer":[36],"can":[37],"cause":[38],"formation":[40],"protein-metal":[42],"complexes":[43],"that":[44,123],"do":[45],"exist":[47],"vivo.":[49],"We":[50,75],"implemented":[51],"a":[52,58,89,167,184,196,218],"deep":[53],"learning":[54],"approach":[55],"to":[56,61,216],"build":[57],"classifier":[59,78,95,105],"able":[60],"distinguish":[62],"between":[63],"physiological":[64,109,239],"and":[65,150,195,203],"adventitious":[66],"zinc-binding":[67],"3D":[71],"metalloproteins.":[74],"trained":[76],"using":[79],"manually":[80],"annotated":[81],"extracted":[83],"from":[84,146,224],"MetalPDB":[86,157],"database.":[87],"Using":[88],"10-fold":[90],"cross":[91],"validation":[92],"procedure,":[93],"achieved":[96],"an":[97,117],"accuracy":[98,118],"about":[100],"90%.":[101],"The":[102],"same":[103],"neural":[104],"could":[106],"predict":[107],"relevance":[110,240],"non-heme":[112],"mononuclear":[113],"iron":[114],"with":[116,177],"nearly":[120],"80%,":[121],"suggesting":[122],"rules":[125],"learned":[126],"on":[127,211],"zinc":[128,144],"have":[130,217],"general":[131],"relevance.":[132],"By":[133],"quantifying":[134],"relative":[136],"importance":[137],"features":[140],"describing":[141],"input":[143],"network":[148],"perspective":[149],"by":[151],"analyzing":[152],"characteristics":[154],"datasets,":[158],"we":[159],"inferred":[160],"some":[161],"common":[162],"principles.":[163],"Physiological":[164],"low":[168,219],"solvent":[169],"accessibility":[170],"aminoacids":[173],"forming":[174],"coordination":[175],"bonds":[176],"ion":[180],"(the":[181],"ligands),":[183],"relatively":[185],"large":[186],"number":[187,220],"residues":[189,205],"environment":[193],"(\u226520),":[194],"distinct":[197],"pattern":[198],"conservation":[200],"Cys":[202],"His":[204],"site.":[208],"Adventitious":[209],"sites,":[210],"other":[213],"hand,":[214],"tend":[215],"donor":[222],"atoms":[223],"polypeptide":[226],"chain":[227],"(often":[228],"two).":[231],"These":[232],"observations":[233],"support":[234],"evaluation":[236],"novel":[242],"metal-binding":[243],"structures.":[247]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}