{"id":"https://openalex.org/W2053486065","doi":"https://doi.org/10.1021/ci100392q","title":"A Simple Protocol for the Comparative Analysis of the Structure and Occurrence of Biochemical Pathways Across Superkingdoms","display_name":"A Simple Protocol for the Comparative Analysis of the Structure and Occurrence of Biochemical Pathways Across Superkingdoms","publication_year":2011,"publication_date":"2011-03-10","ids":{"openalex":"https://openalex.org/W2053486065","doi":"https://doi.org/10.1021/ci100392q","mag":"2053486065","pmid":"https://pubmed.ncbi.nlm.nih.gov/21388232"},"language":"en","primary_location":{"id":"doi:10.1021/ci100392q","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci100392q","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"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":false,"raw_author_name":"Claudia Andreini","raw_affiliation_strings":["Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy"],"raw_orcid":null,"affiliations":[{"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 L. Sacconi 6, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016319366","display_name":"Ivano Bertini","orcid":"https://orcid.org/0000-0002-0616-2444"},"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":"Ivano Bertini","raw_affiliation_strings":["Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy"],"raw_orcid":null,"affiliations":[{"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 L. Sacconi 6, 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":["Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006299389","display_name":"Leonardo Decaria","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":"Leonardo Decaria","raw_affiliation_strings":["Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Magnetic Resonance Center (CERM), University of Florence, Via L. 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":false,"raw_author_name":"Antonio Rosato","raw_affiliation_strings":["Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy"],"raw_orcid":null,"affiliations":[{"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 L. Sacconi 6, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5016319366"],"corresponding_institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"],"apc_list":null,"apc_paid":null,"fwci":0.5323,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.65779785,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"51","issue":"3","first_page":"730","last_page":"738"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9994999766349792,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9994999766349792,"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":0.9994000196456909,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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/computer-science","display_name":"Computer science","score":0.6793041825294495},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5434998273849487},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.5192130208015442},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.45580554008483887},{"id":"https://openalex.org/keywords/informatics","display_name":"Informatics","score":0.4333397150039673},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4266425669193268},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.42141813039779663},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4153668284416199},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.40685760974884033},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2100740373134613},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1687469482421875},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1474258005619049},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10204759240150452}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6793041825294495},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5434998273849487},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.5192130208015442},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.45580554008483887},{"id":"https://openalex.org/C191630685","wikidata":"https://www.wikidata.org/wiki/Q4027615","display_name":"Informatics","level":2,"score":0.4333397150039673},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4266425669193268},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.42141813039779663},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4153668284416199},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.40685760974884033},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2100740373134613},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1687469482421875},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1474258005619049},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10204759240150452},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0}],"mesh":[{"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci100392q","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci100392q","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:21388232","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21388232","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:2158/423904","is_oa":false,"landing_page_url":"http://hdl.handle.net/2158/423904","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"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1486453207","https://openalex.org/W1762630411","https://openalex.org/W1964796427","https://openalex.org/W1980578041","https://openalex.org/W1993366463","https://openalex.org/W1995117714","https://openalex.org/W1996529795","https://openalex.org/W1999895438","https://openalex.org/W2014781636","https://openalex.org/W2017583902","https://openalex.org/W2020551149","https://openalex.org/W2021628095","https://openalex.org/W2046618236","https://openalex.org/W2049270340","https://openalex.org/W2055043387","https://openalex.org/W2057885377","https://openalex.org/W2063194507","https://openalex.org/W2064186839","https://openalex.org/W2065970966","https://openalex.org/W2079048673","https://openalex.org/W2086568203","https://openalex.org/W2089579020","https://openalex.org/W2095387858","https://openalex.org/W2105532922","https://openalex.org/W2106391842","https://openalex.org/W2109715166","https://openalex.org/W2112460093","https://openalex.org/W2123060905","https://openalex.org/W2123555047","https://openalex.org/W2127596034","https://openalex.org/W2129448726","https://openalex.org/W2130479394","https://openalex.org/W2145506897","https://openalex.org/W2146312020","https://openalex.org/W2148000475","https://openalex.org/W2151831732","https://openalex.org/W2155331065","https://openalex.org/W2159482845","https://openalex.org/W2162799538","https://openalex.org/W2168048337","https://openalex.org/W4210400672","https://openalex.org/W4230932396","https://openalex.org/W4240852056","https://openalex.org/W4252706339","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W1585007175","https://openalex.org/W2382521049","https://openalex.org/W2144385241","https://openalex.org/W2165950148","https://openalex.org/W4253593777","https://openalex.org/W2951497643","https://openalex.org/W4300101996","https://openalex.org/W2142393343","https://openalex.org/W3101625811","https://openalex.org/W2338854850"],"abstract_inverted_index":{"A":[0],"biochemical":[1,48],"pathway":[2],"can":[3,35],"be":[4,36,65],"viewed":[5],"as":[6,185,187],"a":[7,14,47,73,105,153,200],"series":[8],"of":[9,17,50,109,123,176,190],"chemical":[10],"reactions":[11],"occurring":[12],"within":[13],"cell,":[15],"each":[16],"which":[18,115],"is":[19,43,82,101,116],"carried":[20],"out":[21],"by":[22,52,165],"one":[23,41,180],"or":[24,30,181],"more":[25,198],"biological":[26],"macromolecules":[27],"(protein,":[28],"RNA,":[29],"complexes":[31],"thereof).":[32],"Computational":[33],"methods":[34],"applied":[37],"to":[38,45,64,127,135,144],"assess":[39],"whether":[40,54],"organism":[42],"able":[44],"perform":[46,128],"process":[49],"interest":[51],"checking":[53],"its":[55,163],"genome":[56],"encodes":[57],"all":[58,129,146],"the":[59,68,78,130,137,158,171,174,188],"components":[60],"that":[61,81,132],"are":[62,133],"known":[63],"necessary":[66],"for":[67,76,173],"task.":[69],"Here":[70],"we":[71,169],"present":[72],"simple":[74],"strategy":[75,100,139],"collecting":[77],"above":[79],"data":[80],"based":[83],"on,":[84],"but":[85],"not":[86],"limited":[87],"to,":[88],"our":[89],"experience":[90],"on":[91],"processes":[92],"involving":[93],"metal":[94],"ions":[95],"and":[96,111,143],"metal-binding":[97],"cofactors.":[98],"The":[99,121],"fully":[102],"implemented":[103],"in":[104,148,194,197],"bioinformatics":[106],"package,":[107],"Retrieval":[108],"Domains":[110],"Genome":[112],"Browsing":[113],"(RDGB),":[114],"available":[117],"from":[118],"http://www.cerm.unifi.it/home/research/genomebrowsing.html":[119],".":[120],"use":[122,164],"RDGB":[124],"allows":[125],"users":[126],"operations":[131],"needed":[134],"implement":[136],"aforementioned":[138],"with":[140,152],"minimal":[141],"intervention":[142],"gather":[145],"results":[147],"an":[149],"ordered":[150],"manner,":[151],"tabular":[154],"summary.":[155],"This":[156],"minimizes":[157],"(bio)informatics":[159],"needed,":[160],"thus":[161],"facilitating":[162],"nonexperts.":[166],"As":[167],"examples,":[168],"analyzed":[170],"pathways":[172],"degradation":[175],"organic":[177],"compounds":[178],"containing":[179],"two":[182],"aromatic":[183],"rings":[184],"well":[186],"distribution":[189],"some":[191],"proteins":[192],"involved":[193],"Cu(A)":[195],"assembly":[196],"than":[199],"thousand":[201],"prokaryotes.":[202]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
