{"id":"https://openalex.org/W4395048825","doi":"https://doi.org/10.1038/s41587-024-02214-2","title":"Computational scoring and experimental evaluation of enzymes generated by neural networks","display_name":"Computational scoring and experimental evaluation of enzymes generated by neural networks","publication_year":2024,"publication_date":"2024-04-23","ids":{"openalex":"https://openalex.org/W4395048825","doi":"https://doi.org/10.1038/s41587-024-02214-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/38653796"},"language":"en","primary_location":{"id":"doi:10.1038/s41587-024-02214-2","doi":"https://doi.org/10.1038/s41587-024-02214-2","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41587-024-02214-2","pdf_url":"https://www.nature.com/articles/s41587-024-02214-2.pdf","source":{"id":"https://openalex.org/S106963461","display_name":"Nature Biotechnology","issn_l":"0733-222X","issn":["0733-222X","1087-0156","1546-1696","2331-3684"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Biotechnology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://www.nature.com/articles/s41587-024-02214-2.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020339193","display_name":"Sean R. Johnson","orcid":"https://orcid.org/0000-0001-8261-9015","observed_orcids":["https://orcid.org/0000-0001-8261-9015"]},"institutions":[{"id":"https://openalex.org/I115020962","display_name":"New England Biolabs (United States)","ror":"https://ror.org/04ywg3445","country_code":"US","type":"company","lineage":["https://openalex.org/I115020962"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sean R. Johnson","raw_affiliation_strings":["New England Biolabs, Ipswich, MA, USA"],"raw_orcid":"https://orcid.org/0000-0001-8261-9015","affiliations":[{"raw_affiliation_string":"New England Biolabs, Ipswich, MA, USA","institution_ids":["https://openalex.org/I115020962"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083600269","display_name":"Xiaozhi Fu","orcid":"https://orcid.org/0000-0002-4465-7528","observed_orcids":["https://orcid.org/0000-0002-4465-7528"]},"institutions":[{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Xiaozhi Fu","raw_affiliation_strings":["Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-4465-7528","affiliations":[{"raw_affiliation_string":"Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden","institution_ids":["https://openalex.org/I66862912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031158270","display_name":"Sandra Viknander","orcid":"https://orcid.org/0000-0003-1809-8627","observed_orcids":["https://orcid.org/0000-0003-1809-8627"]},"institutions":[{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Sandra Viknander","raw_affiliation_strings":["Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden","institution_ids":["https://openalex.org/I66862912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031470537","display_name":"Clara Goldin","orcid":"https://orcid.org/0009-0006-8235-3425","observed_orcids":["https://orcid.org/0009-0006-8235-3425"]},"institutions":[{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Clara Goldin","raw_affiliation_strings":["Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden"],"raw_orcid":"https://orcid.org/0009-0006-8235-3425","affiliations":[{"raw_affiliation_string":"Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden","institution_ids":["https://openalex.org/I66862912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073927766","display_name":"Sarah Monaco","orcid":"https://orcid.org/0009-0004-1503-4737","observed_orcids":["https://orcid.org/0009-0004-1503-4737"]},"institutions":[{"id":"https://openalex.org/I4210160571","display_name":"Invitae (United States)","ror":"https://ror.org/05mt7ye26","country_code":"US","type":"company","lineage":["https://openalex.org/I4210160571"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sarah Monaco","raw_affiliation_strings":["Invitae, San Francisco, CA, USA"],"raw_orcid":"https://orcid.org/0009-0004-1503-4737","affiliations":[{"raw_affiliation_string":"Invitae, San Francisco, CA, USA","institution_ids":["https://openalex.org/I4210160571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007057301","display_name":"Aleksej Zelezniak","orcid":"https://orcid.org/0000-0002-3098-9441","observed_orcids":["https://orcid.org/0000-0002-3098-9441"]},"institutions":[{"id":"https://openalex.org/I173212132","display_name":"Vilnius University","ror":"https://ror.org/03nadee84","country_code":"LT","type":"education","lineage":["https://openalex.org/I173212132"]},{"id":"https://openalex.org/I183935753","display_name":"King's College London","ror":"https://ror.org/0220mzb33","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I183935753"]},{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]}],"countries":["GB","LT","SE"],"is_corresponding":true,"raw_author_name":"Aleksej Zelezniak","raw_affiliation_strings":["Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden. aleksej.zelezniak@chalmers.se","Institute of Biotechnology, Life Sciences Centre, Vilnius University, Vilnius, Lithuania. aleksej.zelezniak@chalmers.se","Randall Centre for Cell & Molecular Biophysics, King's College London, Guy's Campus, London, UK. aleksej.zelezniak@chalmers.se","Institute of Biotechnology, Life Sciences Centre, Vilnius University, Vilnius, Lithuania"],"raw_orcid":"https://orcid.org/0000-0002-3098-9441","affiliations":[{"raw_affiliation_string":"Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden. aleksej.zelezniak@chalmers.se","institution_ids":["https://openalex.org/I66862912"]},{"raw_affiliation_string":"Institute of Biotechnology, Life Sciences Centre, Vilnius University, Vilnius, Lithuania. aleksej.zelezniak@chalmers.se","institution_ids":["https://openalex.org/I173212132"]},{"raw_affiliation_string":"Randall Centre for Cell & Molecular Biophysics, King's College London, Guy's Campus, London, UK. aleksej.zelezniak@chalmers.se","institution_ids":["https://openalex.org/I183935753"]},{"raw_affiliation_string":"Institute of Biotechnology, Life Sciences Centre, Vilnius University, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060834723","display_name":"Kevin Yang","orcid":"https://orcid.org/0000-0001-9045-6826","observed_orcids":["https://orcid.org/0000-0001-9045-6826"]},"institutions":[{"id":"https://openalex.org/I1290206253","display_name":"Microsoft (United States)","ror":"https://ror.org/00d0nc645","country_code":"US","type":"company","lineage":["https://openalex.org/I1290206253"]},{"id":"https://openalex.org/I4400600948","display_name":"Microsoft Research New England (United States)","ror":"https://ror.org/010wkqn50","country_code":"US","type":"company","lineage":["https://openalex.org/I1290206253","https://openalex.org/I4400600948"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kevin K. Yang","raw_affiliation_strings":["Microsoft Research, Cambridge, MA, USA. yang.kevin@microsoft.com","Microsoft Research, Cambridge, MA, USA"],"raw_orcid":"https://orcid.org/0000-0001-9045-6826","affiliations":[{"raw_affiliation_string":"Microsoft Research, Cambridge, MA, USA. yang.kevin@microsoft.com","institution_ids":["https://openalex.org/I1290206253"]},{"raw_affiliation_string":"Microsoft Research, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4400600948"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5007057301","https://openalex.org/A5060834723"],"corresponding_institution_ids":["https://openalex.org/I1290206253","https://openalex.org/I173212132","https://openalex.org/I183935753","https://openalex.org/I4400600948","https://openalex.org/I66862912"],"apc_list":{"value":12290,"currency":"USD","value_usd":12290},"apc_paid":{"value":12290,"currency":"USD","value_usd":12290},"fwci":11.0786,"has_fulltext":true,"cited_by_count":99,"citation_normalized_percentile":{"value":0.99362009,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"43","issue":"3","first_page":"396","last_page":"405"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.6528000235557556,"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":0.6528000235557556,"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":0.26030001044273376,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0494999997317791,"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/enzyme-design","display_name":"enzyme design","score":0.5720000267028809},{"id":"https://openalex.org/keywords/ancestral-sequence-reconstruction","display_name":"ancestral sequence reconstruction","score":0.9039999842643738},{"id":"https://openalex.org/keywords/generative-adversarial-networks","display_name":"generative adversarial networks","score":0.996999979019165},{"id":"https://openalex.org/keywords/protein-language-models","display_name":"protein language models","score":0.9990000128746033},{"id":"https://openalex.org/keywords/in-vitro-enzyme-activity","display_name":"in vitro enzyme activity","score":0.7250000238418579},{"id":"https://openalex.org/keywords/protein-engineering","display_name":"protein engineering","score":0.6600000262260437},{"id":"https://openalex.org/keywords/benchmarking","display_name":"benchmarking","score":0.45100000500679016},{"id":"https://openalex.org/keywords/enzyme-families","display_name":"enzyme families","score":0.37299999594688416}],"concepts":[{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5726553201675415},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5293382406234741},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.5014445781707764},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4724683463573456},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4615386426448822},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3453713059425354},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2581789493560791}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1038/s41587-024-02214-2","doi":"https://doi.org/10.1038/s41587-024-02214-2","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41587-024-02214-2","pdf_url":"https://www.nature.com/articles/s41587-024-02214-2.pdf","source":{"id":"https://openalex.org/S106963461","display_name":"Nature Biotechnology","issn_l":"0733-222X","issn":["0733-222X","1087-0156","1546-1696","2331-3684"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Biotechnology","raw_type":"journal-article"},{"id":"doi:10.1101/2023.03.04.531015","doi":"https://doi.org/10.1101/2023.03.04.531015","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2023.03.04.531015","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2023/04/07/2023.03.04.531015.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:38653796","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38653796","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,"listed_in":[],"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":"Nature biotechnology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11919684","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11919684","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11919684/pdf/41587_2024_Article_2214.pdf","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,"listed_in":[],"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":"Nat Biotechnol","raw_type":"Text"},{"id":"pmh:oai:research.chalmers.se:541029","doi":null,"is_oa":false,"landing_page_url":"https://research.chalmers.se/en/publication/26719d58-6be1-49d3-839a-88f451d1a1f2","pdf_url":null,"source":{"id":"https://openalex.org/S4306402469","display_name":"Chalmers Research (Chalmers University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I66862912","host_organization_name":"Chalmers University of Technology","host_organization_lineage":["https://openalex.org/I66862912"],"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}],"best_oa_location":{"id":"doi:10.1038/s41587-024-02214-2","doi":"https://doi.org/10.1038/s41587-024-02214-2","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41587-024-02214-2","pdf_url":"https://www.nature.com/articles/s41587-024-02214-2.pdf","source":{"id":"https://openalex.org/S106963461","display_name":"Nature Biotechnology","issn_l":"0733-222X","issn":["0733-222X","1087-0156","1546-1696","2331-3684"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Biotechnology","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3321450376","display_name":null,"funder_award_id":"05973","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G3771560830","display_name":null,"funder_award_id":"2018\u201005973","funder_id":"https://openalex.org/F4320321033","funder_display_name":"Svenska Forskningsr\u00e5det Formas"},{"id":"https://openalex.org/G402516054","display_name":null,"funder_award_id":"2022\u201306725","funder_id":"https://openalex.org/F4320321033","funder_display_name":"Svenska Forskningsr\u00e5det Formas"},{"id":"https://openalex.org/G4241870131","display_name":"MetaPlast: Exploiting \"microbial dark matter\" for engineering plastic degradation microbial system","funder_award_id":"2019-01403","funder_id":"https://openalex.org/F4320321033","funder_display_name":"Svenska Forskningsr\u00e5det Formas"},{"id":"https://openalex.org/G4302323072","display_name":"Reliable variation interpretation","funder_award_id":"2019-01403","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G6342055602","display_name":null,"funder_award_id":"2019-01403","funder_id":"https://openalex.org/F4320325677","funder_display_name":"Science for Life Laboratory"},{"id":"https://openalex.org/G712881263","display_name":null,"funder_award_id":"2018-","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G7194981950","display_name":"Using AI to unravel \u201cDNA grammar\u201d for synthetic biology applications","funder_award_id":"2019-05356","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G796431723","display_name":null,"funder_award_id":"201805973","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G8869864247","display_name":"NAISS","funder_award_id":"2022-06725","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"}],"funders":[{"id":"https://openalex.org/F4320308943","display_name":"Microsoft Research","ror":"https://ror.org/00d0nc645"},{"id":"https://openalex.org/F4320321033","display_name":"Svenska Forskningsr\u00e5det Formas","ror":"https://ror.org/03pjs1y45"},{"id":"https://openalex.org/F4320321523","display_name":"Chalmers Tekniska H\u00f6gskola","ror":"https://ror.org/040wg7k59"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"},{"id":"https://openalex.org/F4320325677","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4395048825.pdf","grobid_xml":"https://content.openalex.org/works/W4395048825.grobid-xml"},"referenced_works_count":93,"referenced_works":["https://openalex.org/W1579263673","https://openalex.org/W1760278939","https://openalex.org/W1764939414","https://openalex.org/W1788771833","https://openalex.org/W1971147414","https://openalex.org/W1974749552","https://openalex.org/W1983186463","https://openalex.org/W1984180361","https://openalex.org/W1988654948","https://openalex.org/W1992613346","https://openalex.org/W2015292449","https://openalex.org/W2020887458","https://openalex.org/W2031611770","https://openalex.org/W2038898901","https://openalex.org/W2059010479","https://openalex.org/W2064644853","https://openalex.org/W2066829062","https://openalex.org/W2096525273","https://openalex.org/W2101871915","https://openalex.org/W2108211735","https://openalex.org/W2111973517","https://openalex.org/W2114559206","https://openalex.org/W2124351063","https://openalex.org/W2132926880","https://openalex.org/W2138122982","https://openalex.org/W2138820253","https://openalex.org/W2143210482","https://openalex.org/W2144794655","https://openalex.org/W2160378127","https://openalex.org/W2168268382","https://openalex.org/W2170944677","https://openalex.org/W2253581743","https://openalex.org/W2277953252","https://openalex.org/W2379594833","https://openalex.org/W2408883770","https://openalex.org/W2622814825","https://openalex.org/W2767044445","https://openalex.org/W2792977793","https://openalex.org/W2802730096","https://openalex.org/W2809247618","https://openalex.org/W2913129712","https://openalex.org/W2938803199","https://openalex.org/W2984894304","https://openalex.org/W2992150495","https://openalex.org/W3004726194","https://openalex.org/W3019029735","https://openalex.org/W3035847987","https://openalex.org/W3044778276","https://openalex.org/W3088109935","https://openalex.org/W3095583226","https://openalex.org/W3108101741","https://openalex.org/W3112376646","https://openalex.org/W3121000782","https://openalex.org/W3125063344","https://openalex.org/W3132323068","https://openalex.org/W3135130381","https://openalex.org/W3135175179","https://openalex.org/W3138708387","https://openalex.org/W3146944767","https://openalex.org/W3154275519","https://openalex.org/W3156428263","https://openalex.org/W3164145451","https://openalex.org/W3177828909","https://openalex.org/W3179485843","https://openalex.org/W3205324928","https://openalex.org/W3209435229","https://openalex.org/W4205440119","https://openalex.org/W4205773061","https://openalex.org/W4206087583","https://openalex.org/W4206948363","https://openalex.org/W4210494137","https://openalex.org/W4223581484","https://openalex.org/W4224988655","https://openalex.org/W4281790889","https://openalex.org/W4288066876","https://openalex.org/W4289274885","https://openalex.org/W4296031103","https://openalex.org/W4296032638","https://openalex.org/W4306832864","https://openalex.org/W4307171449","https://openalex.org/W4309485183","https://openalex.org/W4312116066","https://openalex.org/W4312197262","https://openalex.org/W4312197757","https://openalex.org/W4313251027","https://openalex.org/W4318071656","https://openalex.org/W4319061788","https://openalex.org/W4387966974","https://openalex.org/W4388024559","https://openalex.org/W4392302569","https://openalex.org/W6769989246","https://openalex.org/W6791955017","https://openalex.org/W6894039266"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"In":[0],"recent":[1],"years,":[2],"generative":[3,45,51,128],"protein":[4,56,119,129],"sequence":[5,48,130],"models":[6,116,131],"have":[7],"been":[8],"developed":[9,99],"to":[10,34,77,83,134],"sample":[11],"novel":[12],"sequences.":[13],"However,":[14],"predicting":[15,88],"whether":[16],"generated":[17,72],"proteins":[18],"will":[19,117],"fold":[20],"and":[21,54,66,71,115,132],"function":[22],"remains":[23],"challenging.":[24],"We":[25],"evaluate":[26],"a":[27,50,55,100,125],"set":[28],"of":[29,38,96,107],"20":[30],"diverse":[31],"computational":[32,85,101],"metrics":[33,86,114],"assess":[35],"the":[36,78,105],"quality":[37],"enzyme":[39,62,91],"sequences":[40,73,82],"produced":[41],"by":[42,110,122],"three":[43,94],"contrasting":[44],"models:":[46],"ancestral":[47],"reconstruction,":[49],"adversarial":[52],"network":[53],"language":[57],"model.":[58],"Focusing":[59],"on":[60],"two":[61],"families,":[63],"we":[64,98],"expressed":[65],"purified":[67],"over":[68],"500":[69],"natural":[70,81],"with":[74],"70-90%":[75],"identity":[76],"most":[79],"similar":[80],"benchmark":[84,126],"for":[87,127,138],"in":[89],"vitro":[90],"activity.":[92],"Over":[93],"rounds":[95],"experiments,":[97],"filter":[102],"that":[103],"improved":[104],"rate":[106],"experimental":[108,139],"success":[109],"50-150%.":[111],"The":[112],"proposed":[113],"drive":[118],"engineering":[120],"research":[121],"serving":[123],"as":[124],"helping":[133],"select":[135],"active":[136],"variants":[137],"testing.":[140]},"counts_by_year":[{"year":2026,"cited_by_count":32},{"year":2025,"cited_by_count":39},{"year":2024,"cited_by_count":25},{"year":2023,"cited_by_count":3}],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2025-10-10T00:00:00"}