{"id":"https://openalex.org/W4387949845","doi":"https://doi.org/10.1093/bioinformatics/btad653","title":"Hunting down zinc(II)-binding sites in proteins with distance matrices","display_name":"Hunting down zinc(II)-binding sites in proteins with distance matrices","publication_year":2023,"publication_date":"2023-10-25","ids":{"openalex":"https://openalex.org/W4387949845","doi":"https://doi.org/10.1093/bioinformatics/btad653","pmid":"https://pubmed.ncbi.nlm.nih.gov/37878807"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad653","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad653","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/btad653","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/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":"Vincenzo Laveglia","raw_affiliation_strings":["Department of Chemistry, University of Florence , Sesto Fiorentino 50019, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Florence , Sesto Fiorentino 50019, Italy","institution_ids":["https://openalex.org/I45084792"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035239143","display_name":"Milana Bazayeva","orcid":"https://orcid.org/0000-0003-0115-2877"},"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":false,"raw_author_name":"Milana Bazayeva","raw_affiliation_strings":["Department of Chemistry, University of Florence , Sesto Fiorentino 50019, Italy","Magnetic Resonance Center (CERM), University of Florence , Sesto Fiorentino 50019, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Florence , Sesto Fiorentino 50019, Italy","institution_ids":["https://openalex.org/I45084792"]},{"raw_affiliation_string":"Magnetic Resonance Center (CERM), University of Florence , Sesto Fiorentino 50019, 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":false,"raw_author_name":"Claudia Andreini","raw_affiliation_strings":["Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine , Sesto Fiorentino 50019, Italy","Department of Chemistry, University of Florence , Sesto Fiorentino 50019, Italy","Magnetic Resonance Center (CERM), University of Florence , Sesto Fiorentino 50019, Italy"],"affiliations":[{"raw_affiliation_string":"Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine , Sesto Fiorentino 50019, Italy","institution_ids":["https://openalex.org/I4210144939"]},{"raw_affiliation_string":"Department of Chemistry, University of Florence , Sesto Fiorentino 50019, Italy","institution_ids":["https://openalex.org/I45084792"]},{"raw_affiliation_string":"Magnetic Resonance Center (CERM), University of Florence , Sesto Fiorentino 50019, 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":false,"raw_author_name":"Antonio Rosato","raw_affiliation_strings":["Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine , Sesto Fiorentino 50019, Italy","Department of Chemistry, University of Florence , Sesto Fiorentino 50019, Italy","Magnetic Resonance Center (CERM), University of Florence , Sesto Fiorentino 50019, Italy"],"affiliations":[{"raw_affiliation_string":"Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine , Sesto Fiorentino 50019, Italy","institution_ids":["https://openalex.org/I4210144939"]},{"raw_affiliation_string":"Department of Chemistry, University of Florence , Sesto Fiorentino 50019, Italy","institution_ids":["https://openalex.org/I45084792"]},{"raw_affiliation_string":"Magnetic Resonance Center (CERM), University of Florence , Sesto Fiorentino 50019, Italy","institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5038390928"],"corresponding_institution_ids":["https://openalex.org/I45084792"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.9794,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.86650815,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"39","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9994000196456909,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9994000196456909,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9990000128746033,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.995199978351593,"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/organism","display_name":"Organism","score":0.6956617832183838},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.6720070242881775},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6163832545280457},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5539735555648804},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5309994220733643},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5231099128723145},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.47401338815689087},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.46746256947517395},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33374089002609253},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30786198377609253},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2369418740272522},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18263381719589233},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17180368304252625},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1298249363899231},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12404957413673401}],"concepts":[{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.6956617832183838},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.6720070242881775},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6163832545280457},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5539735555648804},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5309994220733643},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5231099128723145},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.47401338815689087},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.46746256947517395},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33374089002609253},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30786198377609253},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2369418740272522},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18263381719589233},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17180368304252625},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1298249363899231},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12404957413673401}],"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad653","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad653","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:37878807","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37878807","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:10630175","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10630175","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10630175/pdf/btad653.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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"},{"id":"pmh:oai:flore.unifi.it:2158/1352495","is_oa":true,"landing_page_url":"https://hdl.handle.net/2158/1352495","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad653","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad653","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/G2687563341","display_name":null,"funder_award_id":"824087","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5933564417","display_name":null,"funder_award_id":"824087","funder_id":"https://openalex.org/F4320319638","funder_display_name":"EOSC-Life"},{"id":"https://openalex.org/G7526249834","display_name":null,"funder_award_id":"IR0000009","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320319638","display_name":"EOSC-Life","ror":null},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W120708166","https://openalex.org/W1788100250","https://openalex.org/W1964613343","https://openalex.org/W1971860749","https://openalex.org/W1979392838","https://openalex.org/W1983259744","https://openalex.org/W1994002004","https://openalex.org/W2005697780","https://openalex.org/W2008466187","https://openalex.org/W2035669377","https://openalex.org/W2042660105","https://openalex.org/W2064186839","https://openalex.org/W2066662117","https://openalex.org/W2070103454","https://openalex.org/W2073798474","https://openalex.org/W2090900194","https://openalex.org/W2097606916","https://openalex.org/W2099672497","https://openalex.org/W2113637265","https://openalex.org/W2171112077","https://openalex.org/W2261645898","https://openalex.org/W2400266494","https://openalex.org/W2472103865","https://openalex.org/W2558889343","https://openalex.org/W2589875042","https://openalex.org/W2742123653","https://openalex.org/W2889619860","https://openalex.org/W2894103608","https://openalex.org/W2895930884","https://openalex.org/W2898210859","https://openalex.org/W2991957026","https://openalex.org/W2993199583","https://openalex.org/W2999044305","https://openalex.org/W3045355728","https://openalex.org/W3116548791","https://openalex.org/W3125208294","https://openalex.org/W3132365153","https://openalex.org/W3143708388","https://openalex.org/W3169686454","https://openalex.org/W3177828909","https://openalex.org/W3203459683","https://openalex.org/W3211795435","https://openalex.org/W4205314965","https://openalex.org/W4231059664","https://openalex.org/W4234165528","https://openalex.org/W4282917556","https://openalex.org/W4285093713","https://openalex.org/W4288690996","https://openalex.org/W4304014809","https://openalex.org/W4310058955","https://openalex.org/W4376225285"],"related_works":["https://openalex.org/W24843447","https://openalex.org/W2361861616","https://openalex.org/W2341492732","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2789551765"],"abstract_inverted_index":{"Master":[0],"of":[1],"Metals":[2],"has":[3],"been":[4],"implemented":[5],"in":[6],"Python":[7],"and":[8],"is":[9],"available":[10],"at":[11],"https://github.com/cerm-cirmmp/Master-of-metals.":[12]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
