{"id":"https://openalex.org/W3041245894","doi":"https://doi.org/10.1021/acs.jcim.0c00489","title":"Improving Enzyme Optimum Temperature Prediction with Resampling Strategies and Ensemble Learning","display_name":"Improving Enzyme Optimum Temperature Prediction with Resampling Strategies and Ensemble Learning","publication_year":2020,"publication_date":"2020-07-08","ids":{"openalex":"https://openalex.org/W3041245894","doi":"https://doi.org/10.1021/acs.jcim.0c00489","mag":"3041245894","pmid":"https://pubmed.ncbi.nlm.nih.gov/32639729"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00489","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00489","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.osti.gov/servlets/purl/1660157","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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"]},{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Japheth E. Gado","raw_affiliation_strings":["Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States","National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States","institution_ids":["https://openalex.org/I143302722"]},{"raw_affiliation_string":"National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States","institution_ids":["https://openalex.org/I1297288678"]}]},{"author_position":"middle","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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gregg T. Beckham","raw_affiliation_strings":["National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States"],"raw_orcid":"https://orcid.org/0000-0002-3480-212X","affiliations":[{"raw_affiliation_string":"National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States","institution_ids":["https://openalex.org/I1297288678"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067524914","display_name":"Christina M. Payne","orcid":"https://orcid.org/0000-0001-5264-0964"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Christina M. Payne","raw_affiliation_strings":["Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States"],"raw_orcid":"https://orcid.org/0000-0001-5264-0964","affiliations":[{"raw_affiliation_string":"Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States","institution_ids":["https://openalex.org/I143302722"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5018268999","https://openalex.org/A5067524914"],"corresponding_institution_ids":["https://openalex.org/I1297288678","https://openalex.org/I143302722"],"apc_list":null,"apc_paid":null,"fwci":2.8349,"has_fulltext":true,"cited_by_count":63,"citation_normalized_percentile":{"value":0.91675726,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"60","issue":"8","first_page":"4098","last_page":"4107"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9876000285148621,"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":0.9876000285148621,"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":0.9804999828338623,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9779999852180481,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/resampling","display_name":"Resampling","score":0.8705506324768066},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.5343116521835327},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.5044745206832886},{"id":"https://openalex.org/keywords/mean-squared-prediction-error","display_name":"Mean squared prediction error","score":0.4721500873565674},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.37029945850372314},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.34771835803985596},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34385451674461365},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3358144164085388},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32253098487854004},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.06980115175247192}],"concepts":[{"id":"https://openalex.org/C150921843","wikidata":"https://www.wikidata.org/wiki/Q1170431","display_name":"Resampling","level":2,"score":0.8705506324768066},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.5343116521835327},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.5044745206832886},{"id":"https://openalex.org/C167085575","wikidata":"https://www.wikidata.org/wiki/Q6803654","display_name":"Mean squared prediction error","level":2,"score":0.4721500873565674},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.37029945850372314},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.34771835803985596},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34385451674461365},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3358144164085388},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32253098487854004},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.06980115175247192},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"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":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.0c00489","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00489","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:32639729","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32639729","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:osti.gov:1660157","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1660157","pdf_url":"https://www.osti.gov/servlets/purl/1660157","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}],"best_oa_location":{"id":"pmh:oai:osti.gov:1660157","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1660157","pdf_url":"https://www.osti.gov/servlets/purl/1660157","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},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1034717831","display_name":null,"funder_award_id":"1552355","funder_id":"https://openalex.org/F4320337390","funder_display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems"},{"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/G1990957049","display_name":null,"funder_award_id":"1552355","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"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/G3260236582","display_name":null,"funder_award_id":"CBET-1552355","funder_id":"https://openalex.org/F4320337390","funder_display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems"},{"id":"https://openalex.org/G3883580859","display_name":null,"funder_award_id":"DE-AC36-08GO28308","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"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/G4785159920","display_name":null,"funder_award_id":"AC36-08GO28308","funder_id":"https://openalex.org/F4320338290","funder_display_name":"National Renewable Energy Laboratory"},{"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/G8846609399","display_name":null,"funder_award_id":"DE-AC36-08GO28308","funder_id":"https://openalex.org/F4320338290","funder_display_name":"National Renewable Energy Laboratory"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332360","display_name":"Office of Energy Efficiency and Renewable Energy","ror":"https://ror.org/02xznz413"},{"id":"https://openalex.org/F4320337390","display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems","ror":"https://ror.org/0471zv972"},{"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},{"id":"https://openalex.org/F4320338290","display_name":"National Renewable Energy Laboratory","ror":"https://ror.org/036266993"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W3041245894.pdf"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W1561774098","https://openalex.org/W1563938718","https://openalex.org/W1572134200","https://openalex.org/W1981306857","https://openalex.org/W1990513442","https://openalex.org/W2006488700","https://openalex.org/W2009373959","https://openalex.org/W2017736462","https://openalex.org/W2018061754","https://openalex.org/W2026343937","https://openalex.org/W2040217813","https://openalex.org/W2047022461","https://openalex.org/W2047444359","https://openalex.org/W2048537773","https://openalex.org/W2058714876","https://openalex.org/W2059185913","https://openalex.org/W2065806863","https://openalex.org/W2072599243","https://openalex.org/W2075845492","https://openalex.org/W2083811115","https://openalex.org/W2096945460","https://openalex.org/W2099454382","https://openalex.org/W2101234009","https://openalex.org/W2102626860","https://openalex.org/W2105981176","https://openalex.org/W2109553965","https://openalex.org/W2113710405","https://openalex.org/W2117190680","https://openalex.org/W2118978333","https://openalex.org/W2120322316","https://openalex.org/W2121519777","https://openalex.org/W2136256517","https://openalex.org/W2137029138","https://openalex.org/W2143994417","https://openalex.org/W2148143831","https://openalex.org/W2161690185","https://openalex.org/W2164330572","https://openalex.org/W2171141701","https://openalex.org/W2171666007","https://openalex.org/W2172034373","https://openalex.org/W2298358682","https://openalex.org/W2338318698","https://openalex.org/W2409717747","https://openalex.org/W2464663739","https://openalex.org/W2490420619","https://openalex.org/W2770630458","https://openalex.org/W2772032254","https://openalex.org/W2781821160","https://openalex.org/W2793168264","https://openalex.org/W2894779738","https://openalex.org/W2899903294","https://openalex.org/W2912783011","https://openalex.org/W2912895282","https://openalex.org/W2937533359","https://openalex.org/W2949670700","https://openalex.org/W2980789587","https://openalex.org/W2997866479","https://openalex.org/W3173502451","https://openalex.org/W4212883601"],"related_works":["https://openalex.org/W2052515325","https://openalex.org/W2050948537","https://openalex.org/W2767646790","https://openalex.org/W2352041579","https://openalex.org/W1488006380","https://openalex.org/W1998176685","https://openalex.org/W2138381686","https://openalex.org/W2141585124","https://openalex.org/W3008199583","https://openalex.org/W2896146092"],"abstract_inverted_index":{"Accurate":[0],"prediction":[1],"of":[2,8,56,63,81,100],"the":[3,70,79,82,85,104,125,131,143,162],"optimal":[4],"catalytic":[5],"temperature":[6,154],"(Topt)":[7],"enzymes":[9,15,157],"is":[10,96],"vital":[11],"in":[12,166],"biotechnology,":[13],"as":[14,175],"with":[16,52,158],"high":[17,134],"Topt":[18,40,55,64,90,135],"values":[19,65,91,107,136],"are":[20,169],"desired":[21],"for":[22,33,38,74,156],"enhanced":[23],"reaction":[24],"rates.":[25],"Recently,":[26],"a":[27,47,53],"machine":[28],"learning":[29,119],"method":[30],"(temperature":[31],"optima":[32,155],"microorganisms":[34],"and":[35,59,110,120,141,161],"enzymes,":[36],"TOME)":[37],"predicting":[39],"was":[41,44],"developed.":[42],"TOME":[43],"trained":[45],"on":[46,89,106,133,178],"normally":[48],"distributed":[49],"data":[50,126],"set":[51],"median":[54],"37":[57],"\u00b0C":[58,95],"less":[60],"than":[61,93,103],"5%":[62],"above":[66],"85":[67,94],"\u00b0C,":[68],"limiting":[69],"method\u2019s":[71],"predictive":[72],"capabilities":[73],"thermostable":[75],"enzymes.":[76],"Due":[77],"to":[78,128,149,172],"distribution":[80],"training":[83],"data,":[84],"mean":[86],"squared":[87],"error":[88,105,132],"greater":[92],"nearly":[97],"an":[98],"order":[99],"magnitude":[101],"higher":[102],"between":[108],"30":[109],"50":[111],"\u00b0C.":[112],"In":[113],"this":[114,167],"study,":[115],"we":[116],"apply":[117],"ensemble":[118],"resampling":[121,159,163],"strategies":[122,164],"that":[123],"tackle":[124],"imbalance":[127],"significantly":[129],"decrease":[130],"(>85":[137],"\u00b0C)":[138],"by":[139],"60%":[140],"increase":[142],"overall":[144],"R2":[145],"value":[146],"from":[147],"0.527":[148],"0.632.":[150],"The":[151],"revised":[152],"method,":[153],"(TOMER),":[160],"applied":[165],"work":[168],"freely":[170],"available":[171],"other":[173],"researchers":[174],"Python":[176],"packages":[177],"GitHub.":[179]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":5}],"updated_date":"2026-06-21T07:57:09.225873","created_date":"2025-10-10T00:00:00"}
