{"id":"https://openalex.org/W2099672497","doi":"https://doi.org/10.1093/bioinformatics/bts246","title":"FindGeo: a tool for determining metal coordination geometry","display_name":"FindGeo: a tool for determining metal coordination geometry","publication_year":2012,"publication_date":"2012-05-03","ids":{"openalex":"https://openalex.org/W2099672497","doi":"https://doi.org/10.1093/bioinformatics/bts246","mag":"2099672497","pmid":"https://pubmed.ncbi.nlm.nih.gov/22556364"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts246","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts246","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1658/48873890/bioinformatics_28_12_1658.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1658/48873890/bioinformatics_28_12_1658.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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":["1 Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. 2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. 2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058680339","display_name":"Gabriele Cavallaro","orcid":"https://orcid.org/0000-0002-3239-9904"},"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":"Gabriele Cavallaro","raw_affiliation_strings":["1 Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. 2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. 2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011905067","display_name":"Serena Lorenzini","orcid":null},"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":"Serena Lorenzini","raw_affiliation_strings":["1 Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. 2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. 2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5079457434"],"corresponding_institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8903,"has_fulltext":false,"cited_by_count":57,"citation_normalized_percentile":{"value":0.73083159,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"12","first_page":"1658","last_page":"1660"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.08349999785423279,"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"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.08349999785423279,"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/T11747","display_name":"Metal-Catalyzed Oxygenation Mechanisms","score":0.07930000126361847,"subfield":{"id":"https://openalex.org/subfields/1604","display_name":"Inorganic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10163","display_name":"Metal complexes synthesis and properties","score":0.06859999895095825,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/coordination-geometry","display_name":"Coordination geometry","score":0.5975219011306763},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5387353301048279},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.4952069818973541},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44359761476516724},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2064962387084961},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18701547384262085},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16113761067390442},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.05293828248977661}],"concepts":[{"id":"https://openalex.org/C194196696","wikidata":"https://www.wikidata.org/wiki/Q1753378","display_name":"Coordination geometry","level":4,"score":0.5975219011306763},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5387353301048279},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.4952069818973541},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44359761476516724},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2064962387084961},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18701547384262085},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16113761067390442},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.05293828248977661},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.0}],"mesh":[{"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":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts246","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts246","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1658/48873890/bioinformatics_28_12_1658.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22556364","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22556364","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:flore.unifi.it:2158/777957","is_oa":false,"landing_page_url":"http://hdl.handle.net/2158/777957","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:zenodo.org:100745","is_oa":true,"landing_page_url":"https://www.openaccessrepository.it/record/100745","pdf_url":null,"source":{"id":"https://openalex.org/S4306402478","display_name":"INFM-OAR (INFN Catania)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210116497","host_organization_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Catania","host_organization_lineage":["https://openalex.org/I4210116497"],"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/bts246","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts246","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1658/48873890/bioinformatics_28_12_1658.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2099672497.pdf"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W615683476","https://openalex.org/W1800266928","https://openalex.org/W1975165348","https://openalex.org/W1983259744","https://openalex.org/W1994002004","https://openalex.org/W2032842297","https://openalex.org/W2034971743","https://openalex.org/W2053673348","https://openalex.org/W2062781904","https://openalex.org/W2066662117","https://openalex.org/W2125696348","https://openalex.org/W2130479394","https://openalex.org/W2147431408","https://openalex.org/W2166159407","https://openalex.org/W4386779419"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W4235527825"],"abstract_inverted_index":{"UNLABELLED:":[0],"Metals":[1],"are":[2,111],"essential":[3],"for":[4],"the":[5,19,34,51,62,78,94,98,117],"structure":[6,100],"and":[7,12,36,64,75,130],"function":[8],"of":[9,18,33,38,61,81,104],"many":[10],"proteins":[11],"nucleic":[13],"acids.":[14],"The":[15],"geometrical":[16],"arrangement":[17],"atoms":[20,96],"that":[21,39],"coordinate":[22],"a":[23,26,87,102,127,132],"metal":[24],"in":[25,86,97],"biological":[27],"macromolecule":[28],"is":[29,123],"an":[30,56],"important":[31],"determinant":[32],"specificity":[35],"role":[37],"metal.":[40],"At":[41],"present,":[42],"however,":[43],"this":[44],"information":[45],"can":[46],"be":[47],"retrieved":[48],"only":[49],"from":[50],"literature,":[52],"which":[53,110],"sometimes":[54],"contains":[55],"improper":[57],"or":[58,83],"incorrect":[59],"description":[60],"geometry,":[63],"often":[65],"lacks":[66],"it":[67],"altogether.":[68],"Thus,":[69],"we":[70],"developed":[71],"FindGeo":[72,90,122],"to":[73,101,115],"quickly":[74],"easily":[76],"determine":[77],"coordination":[79],"geometry":[80,119],"selected,":[82],"all,":[84],"metals":[85],"given":[88],"structure.":[89],"works":[91],"by":[92,113],"superimposing":[93],"metal-coordinating":[95],"input":[99],"library":[103],"templates":[105],"with":[106],"alternative":[107],"ideal":[108],"geometries,":[109],"ranked":[112],"RMSD":[114],"identify":[116],"best":[118],"assignment.":[120],"AVAILABILITY:":[121],"freely":[124],"available":[125],"as":[126,131],"web":[128],"service":[129],"stand-alone":[133],"program":[134],"at":[135],"http://metalweb.cerm.unifi.it/tools/findgeo/.":[136]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
