{"id":"https://openalex.org/W1525523977","doi":null,"title":"Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies.","display_name":"Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies.","publication_year":2002,"publication_date":"2002-01-01","ids":{"openalex":"https://openalex.org/W1525523977","mag":"1525523977","pmid":"https://pubmed.ncbi.nlm.nih.gov/11808871"},"language":"en","primary_location":{"id":"pmid:11808871","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11808871","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"In silico biology","raw_type":"Journal Article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Masami Ikeda","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I173009982","display_name":"Iwate University","ror":"https://ror.org/04cd75h10","country_code":"JP","type":"education","lineage":["https://openalex.org/I173009982"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masami Ikeda","raw_affiliation_strings":["Science of Bioresources Program, The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Science of Bioresources Program, The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan","institution_ids":["https://openalex.org/I173009982"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110257857","display_name":"Masafumi Arai","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Masafumi Arai","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065577437","display_name":"Demelo Madrazo Lao","orcid":"https://orcid.org/0000-0002-0882-2469","observed_orcids":["https://orcid.org/0000-0002-0882-2469"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Demelo M Lao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5046628885","display_name":"Toshio Shimizu","orcid":"https://orcid.org/0000-0001-6632-0638","observed_orcids":["https://orcid.org/0000-0001-6632-0638"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Toshio Shimizu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":4.3023,"has_fulltext":false,"cited_by_count":146,"citation_normalized_percentile":{"value":0.95698254,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"2","issue":"1","first_page":"19","last_page":"33"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9965999722480774,"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":0.9965999722480774,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.00279999990016222,"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":0.00019999999494757503,"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/transmembrane-topology-prediction","display_name":"transmembrane topology prediction","score":0.984000027179718},{"id":"https://openalex.org/keywords/consensus-forecasts","display_name":"consensus forecasts","score":0.8320000171661377},{"id":"https://openalex.org/keywords/hidden-markov-models","display_name":"hidden Markov models","score":0.75},{"id":"https://openalex.org/keywords/tmhmm","display_name":"TMHMM","score":0.6740000247955322},{"id":"https://openalex.org/keywords/eukaryotic-membrane-proteins","display_name":"eukaryotic membrane proteins","score":0.9990000128746033},{"id":"https://openalex.org/keywords/prediction-performance-comparison","display_name":"prediction performance comparison","score":0.3269999921321869}],"concepts":[{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.757904052734375},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.5638751983642578},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5581235289573669},{"id":"https://openalex.org/C198082294","wikidata":"https://www.wikidata.org/wiki/Q3399648","display_name":"Position (finance)","level":2,"score":0.5454675555229187},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.49116250872612},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3606007397174835},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35536277294158936},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34978345036506653},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32911163568496704},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3170154094696045},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.07543662190437317},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"pmid:11808871","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11808871","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"In silico biology","raw_type":"Journal Article"},{"id":"mag:1525523977","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11808871","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":"PubMed","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W7098651063","https://openalex.org/W2143768153","https://openalex.org/W1499831407","https://openalex.org/W7096387885","https://openalex.org/W2112905569","https://openalex.org/W2363531202","https://openalex.org/W2098098021","https://openalex.org/W1963488400","https://openalex.org/W2111119053","https://openalex.org/W1493607203"],"abstract_inverted_index":{"We":[0,81],"selected":[1],"10":[2],"transmembrane":[3,64],"(TM)":[4],"prediction":[5,25,41,46,54,94,119,133,157,161,195,200],"methods":[6,87,91,104,117],"(KKD,":[7],"TMpred,":[8],"TopPred":[9],"II,":[10],"DAS,":[11],"TMAP,":[12],"MEMSAT":[13],"2,":[14],"SOSUI,":[15],"PRED-TMR2,":[16],"TMHMM":[17],"2.0":[18,112],"and":[19,22,52,77,184,187],"HMMTOP":[20,111],"2.0)":[21],"re-assessed":[23],"its":[24],"performance":[26,42,49,95,134,162,201],"using":[27],"a":[28,44],"reliable":[29],"dataset":[30],"with":[31,118,143],"122":[32],"entries":[33],"of":[34,63,70,178,182],"experimentally-characterized":[35],"TM":[36,79,188,222],"topologies.":[37],"Then,":[38],"we":[39],"improved":[40,160,197],"by":[43,92,217],"consensus":[45,53,156,194],"method.":[47],"Prediction":[48],"during":[50],"re-assessment":[51],"were":[55,106,211],"based":[56],"on":[57],"four":[58,98],"attributes:":[59],"(i)":[60],"the":[61,68,137,147,176,199,205],"number":[62,69,177,181],"segments":[65],"(TMSs),":[66],"(ii)":[67],"TMSs":[71],"plus":[72],"TMS-position,":[73],"(iii)":[74],"N-tail":[75],"location":[76],"(iv)":[78],"topology.":[80,223],"noted":[82],"that":[83,153,215],"hidden":[84],"Markov":[85],"model-based":[86],"dominate":[88],"over":[89],"other":[90,116,148],"individual":[93],"for":[96,135,175,208,221],"all":[97,102,127,136,209],"attributes.":[99,128],"In":[100],"addition,":[101],"top-performing":[103],"generally":[105],"model-based.":[107],"Among":[108],"prokaryotic":[109,144,173,218],"sequences,":[110,132,204],"solely":[113],"topped":[114],"among":[115,130,172,202],"accuracies":[120,207],"ranging":[121],"from":[122],"64%":[123],"to":[124],"86%":[125],"across":[126],"However,":[129],"eukaryotic":[131,203],"attributes":[138,190,210],"was":[139],"relatively":[140,212],"poor":[141],"compared":[142],"ones.":[145],"On":[146],"hand,":[149],"our":[150,154,193],"results":[151],"showed":[152],"proposed":[155],"method":[158,196],"significantly":[159],"by,":[163],"at":[164],"least,":[165],"an":[166],"additional":[167],"nine":[168],"percentage":[169],"points":[170],"particularly":[171,220],"sequences":[174],"TMS":[179,183],"(84%),":[180],"position":[185],"(80%),":[186],"topology":[189],"(74%).":[191],"Although":[192],"also":[198],"obtained":[206,216],"lower":[213],"than":[214],"counterparts":[219]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":7}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}