{"id":"https://openalex.org/W2160020195","doi":"https://doi.org/10.1093/bioinformatics/bti126","title":"A simple statistical method for discriminating outer membrane proteins with better accuracy","display_name":"A simple statistical method for discriminating outer membrane proteins with better accuracy","publication_year":2004,"publication_date":"2004-11-05","ids":{"openalex":"https://openalex.org/W2160020195","doi":"https://doi.org/10.1093/bioinformatics/bti126","mag":"2160020195","pmid":"https://pubmed.ncbi.nlm.nih.gov/15531602"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti126","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti126","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046879365","display_name":"M. Michael Gromiha","orcid":"https://orcid.org/0000-0002-1776-4096"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"M. Michael Gromiha","raw_affiliation_strings":["Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) Aomi Frontier Building 17F, 2-43 Aomi, Koto-ku, Tokyo 135-0064, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) Aomi Frontier Building 17F, 2-43 Aomi, Koto-ku, Tokyo 135-0064, Japan","institution_ids":["https://openalex.org/I73613424"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082820710","display_name":"Makiko Suwa","orcid":"https://orcid.org/0000-0001-8812-1023"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Makiko Suwa","raw_affiliation_strings":["Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) Aomi Frontier Building 17F, 2-43 Aomi, Koto-ku, Tokyo 135-0064, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) Aomi Frontier Building 17F, 2-43 Aomi, Koto-ku, Tokyo 135-0064, Japan","institution_ids":["https://openalex.org/I73613424"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5046879365"],"corresponding_institution_ids":["https://openalex.org/I73613424"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.8739,"has_fulltext":false,"cited_by_count":104,"citation_normalized_percentile":{"value":0.91090899,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"21","issue":"7","first_page":"961","last_page":"968"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9991000294685364,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9887999892234802,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/globular-protein","display_name":"Globular protein","score":0.8051204681396484},{"id":"https://openalex.org/keywords/membrane-protein","display_name":"Membrane protein","score":0.7676634788513184},{"id":"https://openalex.org/keywords/bacterial-outer-membrane","display_name":"Bacterial outer membrane","score":0.712928295135498},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.5659587979316711},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.5063654184341431},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49262291193008423},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.44834089279174805},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4156968593597412},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3473580777645111},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.33063456416130066},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3305756449699402},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17069798707962036}],"concepts":[{"id":"https://openalex.org/C105168689","wikidata":"https://www.wikidata.org/wiki/Q901969","display_name":"Globular protein","level":2,"score":0.8051204681396484},{"id":"https://openalex.org/C144647389","wikidata":"https://www.wikidata.org/wiki/Q423042","display_name":"Membrane protein","level":3,"score":0.7676634788513184},{"id":"https://openalex.org/C146587185","wikidata":"https://www.wikidata.org/wiki/Q258248","display_name":"Bacterial outer membrane","level":4,"score":0.712928295135498},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5659587979316711},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.5063654184341431},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49262291193008423},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.44834089279174805},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4156968593597412},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3473580777645111},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.33063456416130066},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3305756449699402},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17069798707962036},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"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":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti126","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti126","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15531602","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15531602","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}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","score":0.6800000071525574,"display_name":"Reduced inequalities"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1481256263","https://openalex.org/W1491063910","https://openalex.org/W1542067597","https://openalex.org/W1605593725","https://openalex.org/W1973468358","https://openalex.org/W1978650123","https://openalex.org/W1998051952","https://openalex.org/W2001793217","https://openalex.org/W2001808731","https://openalex.org/W2039647109","https://openalex.org/W2044514995","https://openalex.org/W2045157845","https://openalex.org/W2062999231","https://openalex.org/W2067918411","https://openalex.org/W2072871401","https://openalex.org/W2074178106","https://openalex.org/W2074398530","https://openalex.org/W2075035438","https://openalex.org/W2075789879","https://openalex.org/W2078697068","https://openalex.org/W2080738203","https://openalex.org/W2085277871","https://openalex.org/W2094966003","https://openalex.org/W2104972430","https://openalex.org/W2105300849","https://openalex.org/W2112227723","https://openalex.org/W2115511385","https://openalex.org/W2117919289","https://openalex.org/W2119587675","https://openalex.org/W2120984924","https://openalex.org/W2122684603","https://openalex.org/W2130479394","https://openalex.org/W2133650672","https://openalex.org/W2137095432","https://openalex.org/W2137382456","https://openalex.org/W2154352662","https://openalex.org/W2155147384","https://openalex.org/W2160072419","https://openalex.org/W2161628345","https://openalex.org/W2163965664","https://openalex.org/W2167393453","https://openalex.org/W2169317607","https://openalex.org/W2191458757","https://openalex.org/W2909347209","https://openalex.org/W2975544349","https://openalex.org/W2976065075","https://openalex.org/W4249100034"],"related_works":["https://openalex.org/W2146899109","https://openalex.org/W2260493136","https://openalex.org/W2135749642","https://openalex.org/W2113188411","https://openalex.org/W4210423528","https://openalex.org/W2095205630","https://openalex.org/W2976965029","https://openalex.org/W2160020195","https://openalex.org/W2023600921","https://openalex.org/W2382178265"],"abstract_inverted_index":{"MOTIVATION:":[0],"Discriminating":[1],"outer":[2,21,55,78,93,108,188],"membrane":[3,12,22,56,79,94,100,109,157,189],"proteins":[4,13,23,49,95,110,134,158,190],"from":[5,24,50,96,191],"other":[6,97,125,171],"folding":[7],"types":[8],"of":[9,32,47,114,120,138,144,163,196],"globular":[10,48,76,98,133],"and":[11,27,35,54,69,77,99,176,201],"is":[14,151,178,206],"an":[15,112,136,161],"important":[16],"task":[17],"both":[18],"for":[19,28,91,116,186,204],"identifying":[20],"genomic":[25,192],"sequences":[26],"the":[29,43,61,107,117,124,132,148,174],"successful":[30],"prediction":[31],"their":[33],"secondary":[34],"tertiary":[36],"structures.":[37],"RESULTS:":[38],"We":[39,58],"have":[40,86],"systematically":[41],"analyzed":[42],"amino":[44],"acid":[45],"composition":[46],"different":[51],"structural":[52,199],"classes":[53],"proteins.":[57,80,101,122,146],"found":[59],"that":[60],"residues,":[62],"Glu,":[63],"His,":[64],"Ile,":[65],"Cys,":[66],"Gln,":[67],"Asn":[68],"Ser,":[70],"show":[71],"a":[72,88,141,179],"significant":[73],"difference":[74],"between":[75],"Based":[81],"on":[82],"this":[83,177],"information,":[84],"we":[85],"devised":[87],"statistical":[89],"method":[90,128,150],"discriminating":[92],"Our":[102],"approach":[103],"correctly":[104,130,154],"picked":[105],"up":[106,159],"with":[111],"accuracy":[113,137,162,166],"89%":[115],"training":[118],"set":[119],"337":[121],"On":[123],"hand,":[126],"our":[127],"has":[129],"excluded":[131],"at":[135],"79%":[139],"in":[140,173],"non-redundant":[142],"dataset":[143],"674":[145],"Furthermore,":[147],"present":[149],"able":[152],"to":[153,160,170],"exclude":[155],"alpha-helical":[156],"80%.":[164],"These":[165],"levels":[167],"are":[168],"comparable":[169],"methods":[172],"literature,":[175],"simple":[180],"method,":[181],"which":[182],"could":[183],"be":[184],"used":[185],"dissecting":[187],"sequences.":[193],"The":[194],"influence":[195],"protein":[197],"size,":[198],"class":[200],"specific":[202],"residues":[203],"discrimination":[205],"discussed.":[207]},"counts_by_year":[{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":6}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
