{"id":"https://openalex.org/W2950327601","doi":"https://doi.org/10.1142/s021972001950029x","title":"Prediction of oxidoreductase subfamily classes based on RFE-SND-CC-PSSM and machine learning methods","display_name":"Prediction of oxidoreductase subfamily classes based on RFE-SND-CC-PSSM and machine learning methods","publication_year":2019,"publication_date":"2019-06-14","ids":{"openalex":"https://openalex.org/W2950327601","doi":"https://doi.org/10.1142/s021972001950029x","mag":"2950327601","pmid":"https://pubmed.ncbi.nlm.nih.gov/31617464"},"language":"en","primary_location":{"id":"doi:10.1142/s021972001950029x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972001950029x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103687341","display_name":"Fang Yuan","orcid":null},"institutions":[{"id":"https://openalex.org/I26080491","display_name":"Kunming Medical University","ror":"https://ror.org/038c3w259","country_code":"CN","type":"education","lineage":["https://openalex.org/I26080491"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fang Yuan","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, School of Basic Medicine, Kunming Medical University, Kunming 650500, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, School of Basic Medicine, Kunming Medical University, Kunming 650500, P. R. China","institution_ids":["https://openalex.org/I26080491"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100726354","display_name":"Gan Liu","orcid":"https://orcid.org/0000-0001-5170-2537"},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gan Liu","raw_affiliation_strings":["Department of Computer Science and Engineering, School of Information Science and Engineering, Yunnan University, Kunming 650504, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, School of Information Science and Engineering, Yunnan University, Kunming 650504, P. R. China","institution_ids":["https://openalex.org/I189210763"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002334286","display_name":"Xiwen Yang","orcid":"https://orcid.org/0000-0003-2012-357X"},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiwen Yang","raw_affiliation_strings":["Department of Computer Science and Engineering, School of Information Science and Engineering, Yunnan University, Kunming 650504, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, School of Information Science and Engineering, Yunnan University, Kunming 650504, P. R. China","institution_ids":["https://openalex.org/I189210763"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040105964","display_name":"Shunfang Wang","orcid":"https://orcid.org/0000-0002-1927-8753"},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shunfang Wang","raw_affiliation_strings":["Department of Computer Science and Engineering, School of Information Science and Engineering, Yunnan University, Kunming 650504, P. R. China"],"raw_orcid":"https://orcid.org/0000-0002-1927-8753","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, School of Information Science and Engineering, Yunnan University, Kunming 650504, P. R. China","institution_ids":["https://openalex.org/I189210763"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030673098","display_name":"Xueren Wang","orcid":"https://orcid.org/0000-0002-8599-8687"},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xueren Wang","raw_affiliation_strings":["School of Mathematics and Statistics, Yunnan University, Kunming 650504, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Yunnan University, Kunming 650504, P. R. China","institution_ids":["https://openalex.org/I189210763"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5040105964"],"corresponding_institution_ids":["https://openalex.org/I189210763"],"apc_list":null,"apc_paid":null,"fwci":0.3436,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.59222142,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"17","issue":"04","first_page":"1950029","last_page":"1950029"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998999834060669,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998999834060669,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9969000220298767,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9922999739646912,"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/artificial-intelligence","display_name":"Artificial intelligence","score":0.6565382480621338},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.612091600894928},{"id":"https://openalex.org/keywords/jackknife-resampling","display_name":"Jackknife resampling","score":0.6039726734161377},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.5523847937583923},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.4913600981235504},{"id":"https://openalex.org/keywords/pseudo-amino-acid-composition","display_name":"Pseudo amino acid composition","score":0.45564067363739014},{"id":"https://openalex.org/keywords/oxidoreductase","display_name":"Oxidoreductase","score":0.45309972763061523},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44188186526298523},{"id":"https://openalex.org/keywords/dipeptide","display_name":"Dipeptide","score":0.35804659128189087},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2364904284477234},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.21698686480522156},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.20704007148742676},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13878199458122253},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.12364569306373596}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6565382480621338},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.612091600894928},{"id":"https://openalex.org/C81790035","wikidata":"https://www.wikidata.org/wiki/Q847158","display_name":"Jackknife resampling","level":3,"score":0.6039726734161377},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5523847937583923},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.4913600981235504},{"id":"https://openalex.org/C2780362125","wikidata":"https://www.wikidata.org/wiki/Q7254464","display_name":"Pseudo amino acid composition","level":4,"score":0.45564067363739014},{"id":"https://openalex.org/C2779268744","wikidata":"https://www.wikidata.org/wiki/Q407479","display_name":"Oxidoreductase","level":3,"score":0.45309972763061523},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44188186526298523},{"id":"https://openalex.org/C2779138802","wikidata":"https://www.wikidata.org/wiki/Q418602","display_name":"Dipeptide","level":3,"score":0.35804659128189087},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2364904284477234},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.21698686480522156},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.20704007148742676},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13878199458122253},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.12364569306373596},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004151","descriptor_name":"Dipeptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004151","descriptor_name":"Dipeptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004151","descriptor_name":"Dipeptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":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":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s021972001950029x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972001950029x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:31617464","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31617464","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 bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.7900000214576721}],"awards":[{"id":"https://openalex.org/G2877240800","display_name":null,"funder_award_id":"2018FE001(-018)","funder_id":"https://openalex.org/F4320332533","funder_display_name":"Applied Basic Research Foundation of Yunnan Province"},{"id":"https://openalex.org/G3050103157","display_name":null,"funder_award_id":"11461079","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3712538734","display_name":null,"funder_award_id":"2017FA032","funder_id":"https://openalex.org/F4320334984","funder_display_name":"Applied Basic Research Key Project of Yunnan"},{"id":"https://openalex.org/G5318167148","display_name":null,"funder_award_id":"11661081","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320332533","display_name":"Applied Basic Research Foundation of Yunnan Province","ror":"https://ror.org/030jhb479"},{"id":"https://openalex.org/F4320334984","display_name":"Applied Basic Research Key Project of Yunnan","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1821507858","https://openalex.org/W1977927254","https://openalex.org/W1980256262","https://openalex.org/W1981722221","https://openalex.org/W1993791542","https://openalex.org/W1998354148","https://openalex.org/W2007828112","https://openalex.org/W2010384668","https://openalex.org/W2026029065","https://openalex.org/W2034070267","https://openalex.org/W2040895929","https://openalex.org/W2048279801","https://openalex.org/W2049617155","https://openalex.org/W2082605863","https://openalex.org/W2083501076","https://openalex.org/W2088253655","https://openalex.org/W2109553965","https://openalex.org/W2110659301","https://openalex.org/W2113077461","https://openalex.org/W2125546020","https://openalex.org/W2128196429","https://openalex.org/W2129508689","https://openalex.org/W2132292391","https://openalex.org/W2133312664","https://openalex.org/W2141437137","https://openalex.org/W2145351317","https://openalex.org/W2145957695","https://openalex.org/W2147580225","https://openalex.org/W2153635508","https://openalex.org/W2201036356","https://openalex.org/W2340907198","https://openalex.org/W2562961196","https://openalex.org/W2608270353","https://openalex.org/W2797342218"],"related_works":["https://openalex.org/W4248520104","https://openalex.org/W4205886662","https://openalex.org/W4362236462","https://openalex.org/W2373289085","https://openalex.org/W1569344764","https://openalex.org/W2592875554","https://openalex.org/W2579432172","https://openalex.org/W2951088188","https://openalex.org/W2063272004","https://openalex.org/W2186226525"],"abstract_inverted_index":{"Oxidoreductase":[0],"is":[1,110,208],"an":[2,11,29,48],"enzyme":[3],"that":[4,192,205],"widely":[5],"exists":[6],"in":[7,14,33],"organisms.":[8],"It":[9],"plays":[10],"important":[12,30],"role":[13],"cellular":[15],"energy":[16],"metabolism":[17],"and":[18,50,74,100,118,120,145,210,213],"biotransformation":[19],"processes.":[20],"Oxidoreductases":[21],"have":[22],"many":[23],"subclasses":[24],"with":[25,141],"different":[26],"functions,":[27],"creating":[28],"classification":[31],"task":[32],"bioinformatics.":[34],"In":[35],"this":[36,171,193],"paper,":[37],"a":[38,131,146],"dataset":[39],"of":[40,54,70,77,83,89,124,166,177,182],"2640":[41],"oxidoreductase":[42,167],"sequences":[43],"was":[44,56],"used":[45,111],"to":[46,58,80,112,129,173,189,198,217],"perform":[47],"analysis":[49],"comparison.":[51],"The":[52,137,202],"idea":[53],"dipeptides":[55],"introduced":[57],"process":[59],"the":[60,81,94,101,116,121,135,142,151,157,164,175,178,218],"Position":[61],"Specific":[62],"Score":[63],"Matrix":[64],"(PSSM),":[65],"since":[66],"each":[67,75],"dipeptide":[68,90],"consists":[69],"two":[71,122],"amino":[72,85],"acids":[73],"column":[76],"PSSM":[78,98,104],"corresponds":[79],"information":[82],"one":[84],"acid.":[86],"Two":[87],"kinds":[88],"scores":[91],"were":[92],"proposed,":[93],"Standardization":[95],"Normal":[96],"Distribution":[97],"(SND-PSSM)":[99],"Correlation":[102],"Coefficient":[103],"(CC-PSSM).":[105],"Recursive":[106],"Feature":[107],"Elimination":[108],"(RFE)":[109],"extract":[113],"features":[114,126],"from":[115],"SND-PSSM":[117],"CC-PSSM,":[119],"sets":[123],"extracted":[125],"are":[127],"combined":[128],"form":[130],"new":[132],"feature":[133],"matrix,":[134],"RFE-SND-CC-PSSM.":[136],"results":[138,203],"show":[139,204],"that,":[140],"proposed":[143],"method":[144,161,172,194,207],"kernel-based":[147],"nonlinear":[148],"SVM":[149],"classifier,":[150],"accuracy":[152,165,188],"can":[153],"reach":[154],"95.56%":[155],"by":[156],"Jackknife":[158],"test.":[159],"Our":[160],"greatly":[162],"improves":[163,185],"subclass":[168],"prediction.":[169],"Using":[170],"predict":[174],"categories":[176],"6":[179],"major":[180],"types":[181],"enzymes":[183],"effectively":[184],"its":[186],"prediction":[187],"94.54%,":[190],"indicating":[191],"has":[195],"general":[196],"applicability":[197],"other":[199],"protein":[200],"problems.":[201],"our":[206],"effective":[209],"universally":[211],"applicable,":[212],"might":[214],"be":[215],"complementary":[216],"existing":[219],"methods.":[220]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}