{"id":"https://openalex.org/W4414466579","doi":"https://doi.org/10.1093/bioinformatics/btaf544","title":"Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE","display_name":"Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE","publication_year":2025,"publication_date":"2025-09-24","ids":{"openalex":"https://openalex.org/W4414466579","doi":"https://doi.org/10.1093/bioinformatics/btaf544","pmid":"https://pubmed.ncbi.nlm.nih.gov/40991335"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf544","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf544","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf544/64373661/btaf544.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","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/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf544/64373661/btaf544.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023289644","display_name":"Evan Komp","orcid":"https://orcid.org/0000-0001-8386-8814"},"institutions":[{"id":"https://openalex.org/I1297288678","display_name":"National Laboratory of the Rockies","ror":"https://ror.org/036266993","country_code":"US","type":"facility","lineage":["https://openalex.org/I1297288678","https://openalex.org/I1330989302","https://openalex.org/I2800842121"]},{"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":"Evan Komp","raw_affiliation_strings":["Agile BioFoundry , Emeryville, CA 94608,","Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory , Golden Colorado, CO 80401,","Agile BioFoundry , Emeryville, CA 94608","Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden Colorado, 80401, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Agile BioFoundry , Emeryville, CA 94608,","institution_ids":["https://openalex.org/I53012624"]},{"raw_affiliation_string":"Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory , Golden Colorado, CO 80401,","institution_ids":["https://openalex.org/I1297288678"]},{"raw_affiliation_string":"Agile BioFoundry , Emeryville, CA 94608","institution_ids":["https://openalex.org/I53012624"]},{"raw_affiliation_string":"Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden Colorado, 80401, United States","institution_ids":["https://openalex.org/I1297288678"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078516822","display_name":"Kristoffer E. Johansson","orcid":"https://orcid.org/0000-0001-6054-0461"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Kristoffer E Johansson","raw_affiliation_strings":["Linderstr\u00f8m-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University of Copenhagen , Copenhagen,","University of Copenhagen Linderstr\u00f8m-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, , Copenhagen,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Linderstr\u00f8m-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University of Copenhagen , Copenhagen,","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"University of Copenhagen Linderstr\u00f8m-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, , Copenhagen,","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083294830","display_name":"Nicholas P. Gauthier","orcid":"https://orcid.org/0000-0002-3680-7514"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas P Gauthier","raw_affiliation_strings":["Department of Data Sciences, Dana-Farber Cancer Institute , Boston, MA 02115,","Department of Systems Biology, Harvard Medical School , Boston, MA 02115,","Harvard Medical School Department of Systems Biology, , Boston, MA 02115","Dana-Farber Cancer Institute Department of Data Sciences, , Boston, MA 02115"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Data Sciences, Dana-Farber Cancer Institute , Boston, MA 02115,","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School , Boston, MA 02115,","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]},{"raw_affiliation_string":"Harvard Medical School Department of Systems Biology, , Boston, MA 02115","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]},{"raw_affiliation_string":"Dana-Farber Cancer Institute Department of Data Sciences, , Boston, MA 02115","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013829048","display_name":"Japheth E. Gado","orcid":"https://orcid.org/0000-0002-0024-2531"},"institutions":[{"id":"https://openalex.org/I1297288678","display_name":"National Laboratory of the Rockies","ror":"https://ror.org/036266993","country_code":"US","type":"facility","lineage":["https://openalex.org/I1297288678","https://openalex.org/I1330989302","https://openalex.org/I2800842121"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Japheth E Gado","raw_affiliation_strings":["Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory , Golden Colorado, CO 80401,","Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden Colorado, 80401, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory , Golden Colorado, CO 80401,","institution_ids":["https://openalex.org/I1297288678"]},{"raw_affiliation_string":"Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden Colorado, 80401, United States","institution_ids":["https://openalex.org/I1297288678"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019872729","display_name":"Kresten Lindorff\u2010Larsen","orcid":"https://orcid.org/0000-0002-4750-6039"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Kresten Lindorff-Larsen","raw_affiliation_strings":["Linderstr\u00f8m-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University of Copenhagen , Copenhagen,","University of Copenhagen Linderstr\u00f8m-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, , Copenhagen,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Linderstr\u00f8m-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University of Copenhagen , Copenhagen,","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"University of Copenhagen Linderstr\u00f8m-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, , Copenhagen,","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018268999","display_name":"Gregg T. Beckham","orcid":"https://orcid.org/0000-0002-3480-212X"},"institutions":[{"id":"https://openalex.org/I1297288678","display_name":"National Laboratory of the Rockies","ror":"https://ror.org/036266993","country_code":"US","type":"facility","lineage":["https://openalex.org/I1297288678","https://openalex.org/I1330989302","https://openalex.org/I2800842121"]},{"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":"Gregg T Beckham","raw_affiliation_strings":["Agile BioFoundry , Emeryville, CA 94608,","Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory , Golden Colorado, CO 80401,","Agile BioFoundry , Emeryville, CA 94608","Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden Colorado, 80401, United States"],"raw_orcid":"https://orcid.org/0000-0002-3480-212X","affiliations":[{"raw_affiliation_string":"Agile BioFoundry , Emeryville, CA 94608,","institution_ids":["https://openalex.org/I53012624"]},{"raw_affiliation_string":"Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory , Golden Colorado, CO 80401,","institution_ids":["https://openalex.org/I1297288678"]},{"raw_affiliation_string":"Agile BioFoundry , Emeryville, CA 94608","institution_ids":["https://openalex.org/I53012624"]},{"raw_affiliation_string":"Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden Colorado, 80401, United States","institution_ids":["https://openalex.org/I1297288678"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.19476538,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.3982999920845032,"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":0.3982999920845032,"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":0.37040001153945923,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.03189999982714653,"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/python","display_name":"Python (programming language)","score":0.9103000164031982},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.6223000288009644},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4966000020503998},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4884999990463257},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.33320000767707825},{"id":"https://openalex.org/keywords/execution-time","display_name":"Execution time","score":0.3138999938964844}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9103000164031982},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8090999722480774},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.6614999771118164},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.6223000288009644},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4966000020503998},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4884999990463257},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.33320000767707825},{"id":"https://openalex.org/C2989134064","wikidata":"https://www.wikidata.org/wiki/Q288510","display_name":"Execution time","level":2,"score":0.3138999938964844},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.31360000371932983},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.3133000135421753},{"id":"https://openalex.org/C2984968299","wikidata":"https://www.wikidata.org/wiki/Q1077784","display_name":"Software tool","level":3,"score":0.28060001134872437},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.25920000672340393},{"id":"https://openalex.org/C2988963302","wikidata":"https://www.wikidata.org/wiki/Q629206","display_name":"Program code","level":2,"score":0.25099998712539673}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":"D012984","descriptor_name":"Software","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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf544","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf544","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf544/64373661/btaf544.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40991335","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40991335","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:11360907","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12553329","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/c42f3cc1-906d-4e20-9239-a2a947b315e0","is_oa":true,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/c42f3cc1-906d-4e20-9239-a2a947b315e0","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"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":"Komp , E , Johansson , K E , Gauthier , N P , Gado , J E , Lindorff-Larsen , K & Beckham , G T 2025 , ' Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE ' , Bioinformatics , vol. 41 , no. 10 , btaf544 . https://doi.org/10.1093/bioinformatics/btaf544","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf544","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf544","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf544/64373661/btaf544.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1304107674","display_name":null,"funder_award_id":"DE-AC36-08GO28308","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1753948535","display_name":null,"funder_award_id":"AC36-08GO28308","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1952009044","display_name":null,"funder_award_id":"DE-AC36-08GO28308","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G2673887332","display_name":null,"funder_award_id":"DE-SC0023278","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2973709321","display_name":null,"funder_award_id":"AC36-08GO28308","funder_id":"https://openalex.org/F4320332360","funder_display_name":"Office of Energy Efficiency and Renewable Energy"},{"id":"https://openalex.org/G4155743553","display_name":null,"funder_award_id":"DE-AC36-08GO28308","funder_id":"https://openalex.org/F4320332360","funder_display_name":"Office of Energy Efficiency and Renewable Energy"},{"id":"https://openalex.org/G4614743091","display_name":null,"funder_award_id":"DE-SC0022024","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G5125914200","display_name":null,"funder_award_id":"DE-SC0023278","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G5698664717","display_name":null,"funder_award_id":"Contract No.  DE-AC36-08GO28308","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6005700546","display_name":null,"funder_award_id":"-AC36-08GO28308","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7021897321","display_name":null,"funder_award_id":"08GO28308","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7744990904","display_name":null,"funder_award_id":"DE-AC36-08GO28308","funder_id":"https://openalex.org/F4320337708","funder_display_name":"Bioenergy Technologies Office"},{"id":"https://openalex.org/G834333836","display_name":null,"funder_award_id":"DE-AC36-08GO28308","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G8538192389","display_name":null,"funder_award_id":"NNF18OC0033950","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320316867","display_name":"Agile BioFoundry","ror":null},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"},{"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/F4320337708","display_name":"Bioenergy Technologies Office","ror":null},{"id":"https://openalex.org/F4320337919","display_name":"Office of Energy Efficiency","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414466579.pdf","grobid_xml":"https://content.openalex.org/works/W4414466579.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W2014159272","https://openalex.org/W2098869926","https://openalex.org/W2137837900","https://openalex.org/W2138122982","https://openalex.org/W2156454061","https://openalex.org/W2245592118","https://openalex.org/W2804523481","https://openalex.org/W2917580301","https://openalex.org/W2950954328","https://openalex.org/W3117256196","https://openalex.org/W3127222570","https://openalex.org/W3157437194","https://openalex.org/W3177500196","https://openalex.org/W3178295718","https://openalex.org/W3179485843","https://openalex.org/W3185856877","https://openalex.org/W3194729882","https://openalex.org/W3209435229","https://openalex.org/W3214130279","https://openalex.org/W4206087583","https://openalex.org/W4225460848","https://openalex.org/W4225868104","https://openalex.org/W4281648132","https://openalex.org/W4295312788","https://openalex.org/W4295749382","https://openalex.org/W4296032638","https://openalex.org/W4309485183","https://openalex.org/W4367183963","https://openalex.org/W4387424814","https://openalex.org/W4391849830","https://openalex.org/W4392041393","https://openalex.org/W4393055192","https://openalex.org/W4396895148","https://openalex.org/W4401071498","https://openalex.org/W4404124421","https://openalex.org/W4406440058","https://openalex.org/W4409952824","https://openalex.org/W4413968075"],"related_works":[],"abstract_inverted_index":{"SUMMARY:":[0],"Protein":[1],"property":[2,45],"prediction":[3,46],"via":[4],"machine":[5],"learning":[6],"with":[7,73],"and":[8,20,39,43,50,76,92,94,100,117,131,136],"without":[9,114],"labeled":[10],"data":[11],"is":[12,82,95],"becoming":[13],"increasingly":[14],"powerful,":[15],"yet":[16],"methods":[17,47],"are":[18],"disparate":[19],"capabilities":[21],"vary":[22],"widely":[23],"over":[24],"applications.":[25],"The":[26,121],"software":[27],"presented":[28],"here,":[29],"\"Artificial":[30],"Intelligence":[31],"Driven":[32],"protein":[33],"Estimation":[34],"(AIDE)\",":[35],"enables":[36],"instantiating,":[37],"optimizing,":[38],"testing":[40],"many":[41],"zero-shot":[42],"supervised":[44],"for":[48],"variants":[49],"variable":[51],"length":[52],"homologs":[53],"in":[54],"a":[55,63,115,132],"single,":[56],"reproducible":[57],"notebook":[58],"or":[59],"script":[60],"by":[61],"defining":[62],"modular,":[64],"standardized":[65],"application":[66],"programming":[67],"interface":[68],"(API),":[69],"i.e.":[70],"drop-in":[71],"compatible":[72],"scikit-learn":[74,90],"transformers":[75],"pipelines.":[77],"AVAILABILITY":[78],"AND":[79],"IMPLEMENTATION:":[80],"AIDE":[81,109],"an":[83],"installable,":[84],"importable":[85],"python":[86],"package":[87],"inheriting":[88],"from":[89],"classes":[91],"API":[93,137],"installable":[96],"on":[97,156],"Windows,":[98],"Mac,":[99],"Linux.":[101],"Many":[102],"of":[103,146,151],"the":[104,149],"wrapped":[105],"models":[106],"internal":[107],"to":[108],"will":[110],"be":[111,127,140,154],"effectively":[112],"inaccessible":[113],"GPU,":[116],"some":[118],"assume":[119],"CUDA.":[120],"newest":[122],"stable,":[123],"tested":[124],"version":[125],"can":[126,139,153],"found":[128,141,155],"at":[129,142,148],"https://github.com/beckham-lab/aide_predict":[130],"full":[133],"user":[134],"guide":[135],"reference":[138],"https://beckham-lab.github.io/aide_predict/.":[143],"Static":[144],"versions":[145],"both":[147],"time":[150],"writing":[152],"Zenodo.":[157]},"counts_by_year":[],"updated_date":"2026-06-21T07:57:09.225873","created_date":"2025-10-10T00:00:00"}
