{"id":"https://openalex.org/W4309768142","doi":"https://doi.org/10.1093/nar/gkac1075","title":"ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design","display_name":"ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design","publication_year":2022,"publication_date":"2022-11-23","ids":{"openalex":"https://openalex.org/W4309768142","doi":"https://doi.org/10.1093/nar/gkac1075","pmid":"https://pubmed.ncbi.nlm.nih.gov/36416273"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkac1075","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac1075","pdf_url":"https://academic.oup.com/nar/article-pdf/51/D1/D532/48440547/gkac1075.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/51/D1/D532/48440547/gkac1075.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069843830","display_name":"Xavier B. Tao","orcid":"https://orcid.org/0009-0003-0964-2296"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xavier B Tao","raw_affiliation_strings":["Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley , CA \u00a094720, USA","Department of Chemistry, University of California , Berkeley , CA \u00a094720, USA"],"affiliations":[{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley , CA \u00a094720, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Department of Chemistry, University of California , Berkeley , CA \u00a094720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035383654","display_name":"Sarah LaFrance","orcid":null},"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/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I53012624","display_name":"Joint BioEnergy Institute","ror":"https://ror.org/03ww55028","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I53012624"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sarah LaFrance","raw_affiliation_strings":["Biofuels and Bioproducts Division, Joint BioEnergy Institute , 5885 Hollis Street , Emeryville , CA \u00a094608, USA","Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley , CA \u00a094720, USA","QB3 Institute, University of California , Berkeley , CA \u00a094720, USA"],"affiliations":[{"raw_affiliation_string":"Biofuels and Bioproducts Division, Joint BioEnergy Institute , 5885 Hollis Street , Emeryville , CA \u00a094608, USA","institution_ids":["https://openalex.org/I53012624"]},{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley , CA \u00a094720, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"QB3 Institute, University of California , Berkeley , CA \u00a094720, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045346394","display_name":"Yifei Xing","orcid":"https://orcid.org/0000-0002-5206-9515"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yifei Xing","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California , Berkeley , CA \u00a094720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California , Berkeley , CA \u00a094720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051167729","display_name":"Alberto A. Nava","orcid":"https://orcid.org/0000-0002-0172-4145"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alberto A Nava","raw_affiliation_strings":["Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley , CA \u00a094720, USA","Department of Chemical and Biomolecular Engineering, University of California , Berkeley , CA \u00a094720, USA"],"affiliations":[{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley , CA \u00a094720, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering, University of California , Berkeley , CA \u00a094720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003905928","display_name":"H\u00e9ctor Garc\u00eda Mart\u00edn","orcid":"https://orcid.org/0000-0002-4556-9685"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I53012624","display_name":"Joint BioEnergy Institute","ror":"https://ror.org/03ww55028","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I53012624"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hector\u00a0Garcia Martin","raw_affiliation_strings":["Biofuels and Bioproducts Division, Joint BioEnergy Institute , 5885 Hollis Street , Emeryville , CA \u00a094608, USA","Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley , CA \u00a094720, USA","Department of Energy Agile BioFoundry , Emeryville , CA \u00a094608, USA"],"affiliations":[{"raw_affiliation_string":"Biofuels and Bioproducts Division, Joint BioEnergy Institute , 5885 Hollis Street , Emeryville , CA \u00a094608, USA","institution_ids":["https://openalex.org/I53012624"]},{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley , CA \u00a094720, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Department of Energy Agile BioFoundry , Emeryville , CA \u00a094608, USA","institution_ids":["https://openalex.org/I53012624"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000312223","display_name":"Jay D. Keasling","orcid":"https://orcid.org/0000-0003-4170-6088"},"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/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]},{"id":"https://openalex.org/I53012624","display_name":"Joint BioEnergy Institute","ror":"https://ror.org/03ww55028","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I53012624"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["CN","DK","US"],"is_corresponding":false,"raw_author_name":"Jay\u00a0D Keasling","raw_affiliation_strings":["Biofuels and Bioproducts Division, Joint BioEnergy Institute , 5885 Hollis Street , Emeryville , CA \u00a094608, USA","Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley , CA \u00a094720, USA","Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies , Shenzhen , China","Department of Bioengineering, University of California , Berkeley , CA \u00a094720, USA","Department of Chemical and Biomolecular Engineering, University of California , Berkeley , CA \u00a094720, USA","Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark \u00a0 2800 Copenhagen , Denmark","QB3 Institute, University of California , Berkeley , CA \u00a094720, USA","Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"Biofuels and Bioproducts Division, Joint BioEnergy Institute , 5885 Hollis Street , Emeryville , CA \u00a094608, USA","institution_ids":["https://openalex.org/I53012624"]},{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley , CA \u00a094720, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies , Shenzhen , China","institution_ids":["https://openalex.org/I4210145761"]},{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley , CA \u00a094720, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering, University of California , Berkeley , CA \u00a094720, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark \u00a0 2800 Copenhagen , Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]},{"raw_affiliation_string":"QB3 Institute, University of California , Berkeley , CA \u00a094720, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I95457486"]},{"raw_affiliation_string":"Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China","institution_ids":["https://openalex.org/I4210145761"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031739103","display_name":"Tyler W. H. Backman","orcid":"https://orcid.org/0000-0002-6056-353X"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I53012624","display_name":"Joint BioEnergy Institute","ror":"https://ror.org/03ww55028","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I53012624"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tyler\u00a0W H Backman","raw_affiliation_strings":["Biofuels and Bioproducts Division, Joint BioEnergy Institute , 5885 Hollis Street , Emeryville , CA \u00a094608, USA","Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley , CA \u00a094720, USA"],"affiliations":[{"raw_affiliation_string":"Biofuels and Bioproducts Division, Joint BioEnergy Institute , 5885 Hollis Street , Emeryville , CA \u00a094608, USA","institution_ids":["https://openalex.org/I53012624"]},{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley , CA \u00a094720, USA","institution_ids":["https://openalex.org/I148283060"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5031739103"],"corresponding_institution_ids":["https://openalex.org/I148283060","https://openalex.org/I53012624"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":4.706,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.95440504,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"51","issue":"D1","first_page":"D532","last_page":"D538"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9936000108718872,"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/T10076","display_name":"Plant-Microbe Interactions and Immunity","score":0.9686999917030334,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/nonribosomal-peptide","display_name":"Nonribosomal peptide","score":0.9304189682006836},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.9050180912017822},{"id":"https://openalex.org/keywords/polyketide-synthase","display_name":"Polyketide synthase","score":0.8291423916816711},{"id":"https://openalex.org/keywords/polyketide","display_name":"Polyketide","score":0.8256413340568542},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.5260736346244812},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32793307304382324},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3234018087387085},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.27738887071609497},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.27180612087249756},{"id":"https://openalex.org/keywords/biosynthesis","display_name":"Biosynthesis","score":0.21863481402397156}],"concepts":[{"id":"https://openalex.org/C2777379556","wikidata":"https://www.wikidata.org/wiki/Q1443801","display_name":"Nonribosomal peptide","level":4,"score":0.9304189682006836},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9050180912017822},{"id":"https://openalex.org/C2777763344","wikidata":"https://www.wikidata.org/wiki/Q4369963","display_name":"Polyketide synthase","level":5,"score":0.8291423916816711},{"id":"https://openalex.org/C2778635478","wikidata":"https://www.wikidata.org/wiki/Q516751","display_name":"Polyketide","level":4,"score":0.8256413340568542},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.5260736346244812},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32793307304382324},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3234018087387085},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.27738887071609497},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.27180612087249756},{"id":"https://openalex.org/C553450214","wikidata":"https://www.wikidata.org/wiki/Q851162","display_name":"Biosynthesis","level":3,"score":0.21863481402397156}],"mesh":[{"descriptor_ui":"D001709","descriptor_name":"Biotechnology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001709","descriptor_name":"Biotechnology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001709","descriptor_name":"Biotechnology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010453","descriptor_name":"Peptide Synthases","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D010453","descriptor_name":"Peptide Synthases","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D010453","descriptor_name":"Peptide Synthases","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D010453","descriptor_name":"Peptide Synthases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010453","descriptor_name":"Peptide Synthases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010453","descriptor_name":"Peptide Synthases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010453","descriptor_name":"Peptide Synthases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010453","descriptor_name":"Peptide Synthases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010453","descriptor_name":"Peptide Synthases","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D048630","descriptor_name":"Polyketide Synthases","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D048630","descriptor_name":"Polyketide Synthases","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D048630","descriptor_name":"Polyketide Synthases","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D048630","descriptor_name":"Polyketide Synthases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D048630","descriptor_name":"Polyketide Synthases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D048630","descriptor_name":"Polyketide Synthases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D048630","descriptor_name":"Polyketide Synthases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D048630","descriptor_name":"Polyketide Synthases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D048630","descriptor_name":"Polyketide Synthases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":9,"locations":[{"id":"doi:10.1093/nar/gkac1075","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac1075","pdf_url":"https://academic.oup.com/nar/article-pdf/51/D1/D532/48440547/gkac1075.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:36416273","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36416273","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt1kv550zd","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/1kv550zd","pdf_url":"https://escholarship.org/content/qt1kv550zd/qt1kv550zd.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, vol 51, iss D1","raw_type":"article"},{"id":"pmh:ark:/13030/qt1kv550zd","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:osti.gov:1899641","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1899641","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:osti.gov:1987508","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1987508","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:osti.gov:2246955","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2246955","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9825560","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825560","pdf_url":null,"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":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:publications/67cefd51-ed96-4e9c-b0b9-dfb8771f9ab5","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/67cefd51-ed96-4e9c-b0b9-dfb8771f9ab5","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"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":"Tao , X B , LaFrance , S , Xing , Y , Nava , A A , Martin , H G , Keasling , J D & Backman , T W H 2023 , ' ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design ' , Nucleic Acids Research , vol. 51 , no. D1 , gkac1075 . https://doi.org/10.1093/nar/gkac1075","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkac1075","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac1075","pdf_url":"https://academic.oup.com/nar/article-pdf/51/D1/D532/48440547/gkac1075.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6227853883","display_name":null,"funder_award_id":"EE0008926","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320318791","display_name":"Philomathia Foundation","ror":null},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320332360","display_name":"Office of Energy Efficiency and Renewable Energy","ror":"https://ror.org/02xznz413"},{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"},{"id":"https://openalex.org/F4320337919","display_name":"Office of Energy Efficiency","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4309768142.pdf","grobid_xml":"https://content.openalex.org/works/W4309768142.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1647671624","https://openalex.org/W1980044767","https://openalex.org/W1995136001","https://openalex.org/W2008387708","https://openalex.org/W2017319656","https://openalex.org/W2041121480","https://openalex.org/W2059719012","https://openalex.org/W2081024217","https://openalex.org/W2089121522","https://openalex.org/W2104619491","https://openalex.org/W2201191303","https://openalex.org/W2220536304","https://openalex.org/W2515002125","https://openalex.org/W2602946330","https://openalex.org/W2606755062","https://openalex.org/W2609551972","https://openalex.org/W2759658772","https://openalex.org/W2763339331","https://openalex.org/W2944857295","https://openalex.org/W2946967855","https://openalex.org/W2949078105","https://openalex.org/W2973114580","https://openalex.org/W2980832688","https://openalex.org/W3022811301","https://openalex.org/W3024254824","https://openalex.org/W3085357237","https://openalex.org/W3095242368","https://openalex.org/W3108757207","https://openalex.org/W3161596995","https://openalex.org/W4283720290","https://openalex.org/W4284883537","https://openalex.org/W4294124094","https://openalex.org/W6636915900","https://openalex.org/W6769413408","https://openalex.org/W6839280580"],"related_works":["https://openalex.org/W2119879182","https://openalex.org/W2016585370","https://openalex.org/W2979795873","https://openalex.org/W2493847578","https://openalex.org/W1964812851","https://openalex.org/W2130896880","https://openalex.org/W2034145103","https://openalex.org/W267089327","https://openalex.org/W2971664913","https://openalex.org/W2465207527"],"abstract_inverted_index":{"Megasynthase":[0],"enzymes":[1,183],"such":[2],"as":[3],"type":[4],"I":[5],"modular":[6,56],"polyketide":[7],"synthases":[8],"(PKSs)":[9],"and":[10,49,55,66,70,85,88,95,101,125,142,151,161],"nonribosomal":[11],"peptide":[12],"synthetases":[13],"(NRPSs)":[14],"play":[15],"a":[16,53,77,133,145],"central":[17],"role":[18],"in":[19,128],"microbial":[20],"chemical":[21,149,176],"warfare":[22],"because":[23],"they":[24],"can":[25,39,179],"evolve":[26],"rapidly":[27],"by":[28,182],"shuffling":[29],"parts":[30],"(catalytic":[31],"domains)":[32],"to":[33,44,58,76,93,130],"produce":[34],"novel":[35],"chemicals.":[36],"If":[37],"we":[38,107],"understand":[40],"the":[41,81,97,109,154,175],"design":[42],"rules":[43],"reshuffle":[45],"these":[46,171],"parts,":[47],"PKSs":[48],"NRPSs":[50],"will":[51],"provide":[52],"systematic":[54],"way":[57],"synthesize":[59],"millions":[60],"of":[61,80,83,99,137,148],"molecules":[62],"including":[63],"pharmaceuticals,":[64],"biomaterials,":[65],"biofuels.":[67],"However,":[68],"PKS":[69,84,104,131],"NRPS":[71,86,126,143],"engineering":[72],"remains":[73],"difficult":[74],"due":[75],"limited":[78],"understanding":[79],"determinants":[82],"fold":[87],"function.":[89],"We":[90],"developed":[91],"ClusterCAD":[92,112,118],"streamline":[94],"simplify":[96],"process":[98],"designing":[100],"testing":[102],"engineered":[103,184],"variants.":[105],"Here,":[106],"present":[108],"highly":[110],"improved":[111],"2.0":[113,119],"release,":[114],"available":[115],"at":[116],"https://clustercad.jbei.org.":[117],"boasts":[120],"support":[121],"for":[122],"PKS-NRPS":[123,140],"hybrid":[124],"clusters":[127],"addition":[129],"clusters;":[132,144],"vastly":[134],"enlarged":[135],"database":[136],"curated":[138],"PKS,":[139],"hybrid,":[141],"diverse":[146],"set":[147],"'starters'":[150],"loading":[152],"modules;":[153],"new":[155],"Domain":[156],"Architecture":[157],"Cluster":[158],"Search":[159],"Tool;":[160],"an":[162],"offline":[163],"Jupyter":[164],"Notebook":[165],"workspace,":[166],"among":[167],"other":[168],"improvements.":[169],"Together":[170],"features":[172],"massively":[173],"expand":[174],"space":[177],"that":[178],"be":[180],"accessed":[181],"with":[185],"ClusterCAD.":[186]},"counts_by_year":[{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":5}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}