{"id":"https://openalex.org/W2078880021","doi":"https://doi.org/10.1371/journal.pcbi.1000700","title":"Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function","display_name":"Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function","publication_year":2010,"publication_date":"2010-03-11","ids":{"openalex":"https://openalex.org/W2078880021","doi":"https://doi.org/10.1371/journal.pcbi.1000700","mag":"2078880021","pmid":"https://pubmed.ncbi.nlm.nih.gov/20300652"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000700","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000700","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000700&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000700&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006111780","display_name":"Daniel E. Almonacid","orcid":"https://orcid.org/0000-0002-1788-2084"},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel E. Almonacid","raw_affiliation_strings":["Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America","California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America","Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I180670191"]},{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082056302","display_name":"Emmanuel R. Yera","orcid":null},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emmanuel R. Yera","raw_affiliation_strings":["Biological and Medical Informatics Graduate Program, University of California San Francisco, San Francisco, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological and Medical Informatics Graduate Program, University of California San Francisco, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046050351","display_name":"John B. O. Mitchell","orcid":"https://orcid.org/0000-0002-0379-6097"},"institutions":[{"id":"https://openalex.org/I16835326","display_name":"University of St Andrews","ror":"https://ror.org/02wn5qz54","country_code":"GB","type":"education","lineage":["https://openalex.org/I16835326"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"John B. O. Mitchell","raw_affiliation_strings":["Centre for Biomolecular Sciences, University of St Andrews, St Andrews, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Biomolecular Sciences, University of St Andrews, St Andrews, United Kingdom","institution_ids":["https://openalex.org/I16835326"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020002876","display_name":"Patricia C. Babbitt","orcid":"https://orcid.org/0000-0003-0375-9015"},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Patricia C. Babbitt","raw_affiliation_strings":["California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America","Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America","Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I180670191"]},{"raw_affiliation_string":"Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I180670191"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5020002876"],"corresponding_institution_ids":["https://openalex.org/I103922791","https://openalex.org/I180670191"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.6148,"has_fulltext":true,"cited_by_count":39,"citation_normalized_percentile":{"value":0.89999131,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"6","issue":"3","first_page":"e1000700","last_page":"e1000700"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991999864578247,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9991999864578247,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9986000061035156,"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/T10404","display_name":"Enzyme Catalysis and Immobilization","score":0.9976000189781189,"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/similarity","display_name":"Similarity (geometry)","score":0.636133074760437},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.59420245885849},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.5450742840766907},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4667022228240967},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.448437362909317},{"id":"https://openalex.org/keywords/catalysis","display_name":"Catalysis","score":0.4203648865222931},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.41511139273643494},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40433862805366516},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.3695841431617737},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36202263832092285},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.29983747005462646},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.22625496983528137},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20972958207130432},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1156022846698761}],"concepts":[{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.636133074760437},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.59420245885849},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.5450742840766907},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4667022228240967},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.448437362909317},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.4203648865222931},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.41511139273643494},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40433862805366516},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3695841431617737},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36202263832092285},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.29983747005462646},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.22625496983528137},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20972958207130432},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1156022846698761},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","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":"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":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004789","descriptor_name":"Enzyme Activation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004789","descriptor_name":"Enzyme Activation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004789","descriptor_name":"Enzyme Activation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004789","descriptor_name":"Enzyme Activation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004789","descriptor_name":"Enzyme Activation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1000700","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000700","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000700&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:20300652","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20300652","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:research-repository.st-andrews.ac.uk:10023/2866","is_oa":true,"landing_page_url":"http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000700","pdf_url":"http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000700","source":{"id":"https://openalex.org/S4306400230","display_name":"St Andrews Research Repository (St Andrews Research Repository)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I16835326","host_organization_name":"University of St Andrews","host_organization_lineage":["https://openalex.org/I16835326"],"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":null,"raw_type":"Journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2837397","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2837397","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.354.4219","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.354.4219","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/8f/c3/PLoS_Comput_Biol_2010_Mar_12_6(3)_e1000700.tar.gz","raw_type":"text"},{"id":"pmh:ark:/13030/qt18c943k3","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:312f6159d3ed44e7988ba47233404af3","is_oa":true,"landing_page_url":"https://doaj.org/article/312f6159d3ed44e7988ba47233404af3","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 6, Iss 3, p e1000700 (2010)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt18c943k3","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/18c943k3","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS computational biology, vol 6, iss 3","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/144253","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Quantitative_Comparison_of_Catalytic_Mechanisms_and_Overall_Reactions_in_Convergently_Evolved_Enzymes_Implications_for_Classification_of_Enzyme_Function/144253","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000700","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000700","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000700&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","score":0.5299999713897705,"display_name":"Peace, Justice and strong institutions"},{"id":"https://metadata.un.org/sdg/10","score":0.47999998927116394,"display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G2534279603","display_name":null,"funder_award_id":"R01GM60595","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2939729635","display_name":"Laying the Foundation of Genomic Enzymology","funder_award_id":"5r01gm060595-16","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5520316217","display_name":null,"funder_award_id":"NIH-R01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6715562766","display_name":null,"funder_award_id":"R01 GM060595","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2078880021.pdf","grobid_xml":"https://content.openalex.org/works/W2078880021.grobid-xml"},"referenced_works_count":127,"referenced_works":["https://openalex.org/W1028073060","https://openalex.org/W1482701468","https://openalex.org/W1529335531","https://openalex.org/W1530704185","https://openalex.org/W1533936090","https://openalex.org/W1597538863","https://openalex.org/W1604281503","https://openalex.org/W1905200960","https://openalex.org/W1948315762","https://openalex.org/W1964640688","https://openalex.org/W1966047992","https://openalex.org/W1966094758","https://openalex.org/W1969172212","https://openalex.org/W1969738839","https://openalex.org/W1970710213","https://openalex.org/W1973275503","https://openalex.org/W1973420497","https://openalex.org/W1978992872","https://openalex.org/W1982785816","https://openalex.org/W1988500898","https://openalex.org/W1989773022","https://openalex.org/W1989837277","https://openalex.org/W1991360268","https://openalex.org/W1995413875","https://openalex.org/W1995808589","https://openalex.org/W1996101432","https://openalex.org/W1996239184","https://openalex.org/W1998532197","https://openalex.org/W2003788979","https://openalex.org/W2004679562","https://openalex.org/W2010297528","https://openalex.org/W2012687647","https://openalex.org/W2013452815","https://openalex.org/W2013776698","https://openalex.org/W2014234027","https://openalex.org/W2014316343","https://openalex.org/W2014547804","https://openalex.org/W2017661263","https://openalex.org/W2019412059","https://openalex.org/W2025425192","https://openalex.org/W2025630877","https://openalex.org/W2034281269","https://openalex.org/W2034349524","https://openalex.org/W2034994407","https://openalex.org/W2040446610","https://openalex.org/W2040633893","https://openalex.org/W2041231457","https://openalex.org/W2041944280","https://openalex.org/W2042116699","https://openalex.org/W2043886357","https://openalex.org/W2043889534","https://openalex.org/W2043972921","https://openalex.org/W2044087102","https://openalex.org/W2044724912","https://openalex.org/W2046116538","https://openalex.org/W2052262181","https://openalex.org/W2052498582","https://openalex.org/W2054699060","https://openalex.org/W2055725315","https://openalex.org/W2056197139","https://openalex.org/W2056799879","https://openalex.org/W2057885377","https://openalex.org/W2058153190","https://openalex.org/W2068018119","https://openalex.org/W2072854916","https://openalex.org/W2074231493","https://openalex.org/W2078286062","https://openalex.org/W2079750630","https://openalex.org/W2082260955","https://openalex.org/W2082593499","https://openalex.org/W2082616165","https://openalex.org/W2085277871","https://openalex.org/W2086503758","https://openalex.org/W2087064593","https://openalex.org/W2088037578","https://openalex.org/W2088755147","https://openalex.org/W2089658775","https://openalex.org/W2094004672","https://openalex.org/W2094414498","https://openalex.org/W2096729078","https://openalex.org/W2097613730","https://openalex.org/W2099389777","https://openalex.org/W2102918317","https://openalex.org/W2103017472","https://openalex.org/W2103310202","https://openalex.org/W2103581950","https://openalex.org/W2103731920","https://openalex.org/W2106375210","https://openalex.org/W2107424557","https://openalex.org/W2108020804","https://openalex.org/W2108067237","https://openalex.org/W2110115297","https://openalex.org/W2112492958","https://openalex.org/W2113014507","https://openalex.org/W2113723577","https://openalex.org/W2114034054","https://openalex.org/W2116258825","https://openalex.org/W2117010916","https://openalex.org/W2118099406","https://openalex.org/W2121379133","https://openalex.org/W2127331128","https://openalex.org/W2127563440","https://openalex.org/W2127597332","https://openalex.org/W2134114753","https://openalex.org/W2136134567","https://openalex.org/W2137846744","https://openalex.org/W2140808721","https://openalex.org/W2143011057","https://openalex.org/W2144494426","https://openalex.org/W2146312020","https://openalex.org/W2148604640","https://openalex.org/W2148849489","https://openalex.org/W2149523277","https://openalex.org/W2157447886","https://openalex.org/W2162220273","https://openalex.org/W2163748594","https://openalex.org/W2164837080","https://openalex.org/W2167689124","https://openalex.org/W2169727430","https://openalex.org/W2171345972","https://openalex.org/W2171421143","https://openalex.org/W2171985093","https://openalex.org/W3086983054","https://openalex.org/W4213326998","https://openalex.org/W4246066782","https://openalex.org/W4252706339","https://openalex.org/W7043571410"],"related_works":["https://openalex.org/W2074014730","https://openalex.org/W4292296636","https://openalex.org/W1963790256","https://openalex.org/W1996722392","https://openalex.org/W2090768198","https://openalex.org/W4206415530","https://openalex.org/W2383633458","https://openalex.org/W3194411068","https://openalex.org/W2042007894","https://openalex.org/W2105075449"],"abstract_inverted_index":{"Functionally":[0],"analogous":[1,80,155,270],"enzymes":[2,47,81,83,156,271],"are":[3],"those":[4],"that":[5,254,264,299,308],"catalyze":[6,234],"similar":[7,10,162],"reactions":[8,71,100,236],"on":[9,21,212],"substrates":[11,114],"but":[12],"do":[13,255],"not":[14,256],"share":[15],"common":[16],"ancestry,":[17],"providing":[18],"a":[19],"window":[20],"the":[22,51,94,105,111,158,170,207,228,268],"different":[23],"structural":[24],"strategies":[25],"nature":[26],"has":[27],"used":[28,136,279],"to":[29,39,115,137,169,244,280],"evolve":[30],"required":[31],"catalysts.":[32],"Identification":[33],"and":[34,43,72,140,241],"use":[35],"of":[36,46,59,78,89,98,107,119,122,143,151,153,176,251,283,292,302,311],"this":[37,147],"information":[38],"improve":[40],"reaction":[41,60,192,220,260,303],"classification":[42,291],"computational":[44],"annotation":[45],"newly":[48],"discovered":[49],"in":[50,66,110,126,157,174,202,289],"genome":[52],"projects":[53],"would":[54],"benefit":[55],"from":[56,93,113],"systematic":[57],"determination":[58],"similarities.":[61],"Here,":[62],"we":[63],"quantified":[64],"similarity":[65,118,193,201,221,261,313],"bond":[67,108,123,239],"changes":[68,109,124,240],"for":[69,75,199,267,286,317],"overall":[70,99,163,191,219,235,259],"catalytic":[73],"mechanisms":[74],"95":[76],"pairs":[77,152,180,253],"functionally":[79,154,269],"(non-homologous":[82],"with":[84,178,237],"identical":[85,185,238,246],"first":[86],"three":[87,229],"numbers":[88],"their":[90,290],"EC":[91,284],"codes)":[92],"MACiE":[95],"database.":[96],"Similarity":[97],"was":[101],"computed":[102],"by":[103],"comparing":[104],"sets":[106,121],"transformations":[112],"products.":[116],"For":[117,165,205],"mechanisms,":[120],"occurring":[125],"each":[127],"mechanistic":[128,144,186,200,224,300,312],"step":[129],"were":[130,134],"compared;":[131],"these":[132,166],"similarities":[133],"then":[135],"guide":[138],"global":[139],"local":[141],"alignments":[142],"steps.":[145],"Using":[146,188],"metric,":[148,190],"only":[149],"44%":[150],"dataset":[159],"had":[160],"significantly":[161],"reactions.":[164,294],"enzymes,":[167],"convergence":[168,301],"same":[171],"mechanism":[172],"occurred":[173],"33%":[175],"cases,":[177],"most":[179],"having":[181],"at":[182,265],"least":[183,266],"one":[184],"step.":[187],"our":[189],"serves":[194],"as":[195],"an":[196],"upper":[197],"bound":[198],"functional":[203,318],"analogs.":[204],"example,":[206],"four":[208],"carbon-oxygen":[209],"lyases":[210],"acting":[211],"phosphates":[213],"(EC":[214,232],"4.2.3)":[215],"show":[216,257],"neither":[217],"significant":[218,223,258],"nor":[222],"similarity.":[225],"By":[226],"contrast,":[227],"carboxylic-ester":[230],"hydrolases":[231],"3.1.1)":[233],"have":[242],"converged":[243],"almost":[245],"mechanisms.":[247],"The":[248,295],"large":[249],"proportion":[250],"enzyme":[252,293],"(56%)":[262],"suggests":[263],"studied":[272],"here,":[273],"more":[274],"stringent":[275],"criteria":[276],"could":[277],"be":[278],"refine":[281],"definitions":[282],"sub-subclasses":[285],"improved":[287],"discrimination":[288],"results":[296],"also":[297],"indicate":[298],"steps":[304],"is":[305],"widespread,":[306],"suggesting":[307],"quantitative":[309],"measurement":[310],"can":[314],"inform":[315],"approaches":[316],"annotation.":[319]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":4}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}