{"id":"https://openalex.org/W2109718329","doi":"https://doi.org/10.1093/bioinformatics/btn114","title":"Prediction of the translocon-mediated membrane insertion free energies of protein sequences","display_name":"Prediction of the translocon-mediated membrane insertion free energies of protein sequences","publication_year":2008,"publication_date":"2008-04-03","ids":{"openalex":"https://openalex.org/W2109718329","doi":"https://doi.org/10.1093/bioinformatics/btn114","mag":"2109718329","pmid":"https://pubmed.ncbi.nlm.nih.gov/18388143"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn114","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn114","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/10/1271/49046000/bioinformatics_24_10_1271.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/10/1271/49046000/bioinformatics_24_10_1271.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076008888","display_name":"Yungki Park","orcid":"https://orcid.org/0000-0003-2839-848X"},"institutions":[{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Yungki Park","raw_affiliation_strings":["Center for Bioinformatics, Saarland University, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Saarland University, Germany","institution_ids":["https://openalex.org/I91712215"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082550931","display_name":"Volkhard Helms","orcid":"https://orcid.org/0000-0002-2180-9154"},"institutions":[{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Volkhard Helms","raw_affiliation_strings":["Center for Bioinformatics, Saarland University, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Saarland University, Germany","institution_ids":["https://openalex.org/I91712215"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5082550931"],"corresponding_institution_ids":["https://openalex.org/I91712215"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.9293,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.74003836,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"24","issue":"10","first_page":"1271","last_page":"1277"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9466999769210815,"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":0.9466999769210815,"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":0.02239999920129776,"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":0.009100000374019146,"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/translocon","display_name":"Translocon","score":0.9194942712783813},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.6019272208213806},{"id":"https://openalex.org/keywords/transmembrane-protein","display_name":"Transmembrane protein","score":0.5788706541061401},{"id":"https://openalex.org/keywords/membrane-protein","display_name":"Membrane protein","score":0.5783356428146362},{"id":"https://openalex.org/keywords/biogenesis","display_name":"Biogenesis","score":0.4935203790664673},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4197548031806946},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34931766986846924},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3386063873767853},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3324234187602997},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.21257901191711426},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11277854442596436}],"concepts":[{"id":"https://openalex.org/C199229279","wikidata":"https://www.wikidata.org/wiki/Q610647","display_name":"Translocon","level":4,"score":0.9194942712783813},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.6019272208213806},{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.5788706541061401},{"id":"https://openalex.org/C144647389","wikidata":"https://www.wikidata.org/wiki/Q423042","display_name":"Membrane protein","level":3,"score":0.5783356428146362},{"id":"https://openalex.org/C131934819","wikidata":"https://www.wikidata.org/wiki/Q135390","display_name":"Biogenesis","level":3,"score":0.4935203790664673},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4197548031806946},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34931766986846924},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3386063873767853},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3324234187602997},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.21257901191711426},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11277854442596436},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"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":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"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":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btn114","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn114","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/10/1271/49046000/bioinformatics_24_10_1271.pdf","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:18388143","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18388143","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":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.896.6146","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.896.6146","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2008/04/03/bioinformatics.btn114.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn114","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn114","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/10/1271/49046000/bioinformatics_24_10_1271.pdf","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"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/6","score":0.699999988079071,"display_name":"Clean water and sanitation"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320882","display_name":"Volkswagen Foundation","ror":"https://ror.org/03bsmfz84"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2109718329.pdf","grobid_xml":"https://content.openalex.org/works/W2109718329.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W1480376833","https://openalex.org/W1970999032","https://openalex.org/W1971024387","https://openalex.org/W1971147414","https://openalex.org/W1971419499","https://openalex.org/W1975304761","https://openalex.org/W1991594572","https://openalex.org/W1996478334","https://openalex.org/W2007415752","https://openalex.org/W2008686051","https://openalex.org/W2012604750","https://openalex.org/W2020570580","https://openalex.org/W2025859600","https://openalex.org/W2026907061","https://openalex.org/W2027502020","https://openalex.org/W2034410027","https://openalex.org/W2049562138","https://openalex.org/W2060791849","https://openalex.org/W2065367476","https://openalex.org/W2069888185","https://openalex.org/W2071282889","https://openalex.org/W2073726493","https://openalex.org/W2078619116","https://openalex.org/W2082287275","https://openalex.org/W2085406419","https://openalex.org/W2086747619","https://openalex.org/W2090022310","https://openalex.org/W2097775366","https://openalex.org/W2097870001","https://openalex.org/W2101466114","https://openalex.org/W2106882534","https://openalex.org/W2115303678","https://openalex.org/W2116173027","https://openalex.org/W2119133319","https://openalex.org/W2126609920","https://openalex.org/W2129838159","https://openalex.org/W2143632667","https://openalex.org/W2144112248","https://openalex.org/W2152178770","https://openalex.org/W2152270594","https://openalex.org/W2152770371","https://openalex.org/W2155147384","https://openalex.org/W2156125289","https://openalex.org/W2157177111","https://openalex.org/W2157535945","https://openalex.org/W2158714788","https://openalex.org/W2158906453","https://openalex.org/W2163137692","https://openalex.org/W2165724689","https://openalex.org/W6678558473"],"related_works":["https://openalex.org/W1989969516","https://openalex.org/W2090871962","https://openalex.org/W3157379108","https://openalex.org/W2003246957","https://openalex.org/W2012297432","https://openalex.org/W2747027787","https://openalex.org/W1586225177","https://openalex.org/W1569425958","https://openalex.org/W2132192325","https://openalex.org/W2807099454"],"abstract_inverted_index":{"MOTIVATION:":[0],"Helical":[1],"membrane":[2,29,37,59,81,137,159],"proteins":[3],"(HMPs)":[4],"play":[5],"crucial":[6],"roles":[7],"in":[8,168],"a":[9,73,92,110,180],"variety":[10],"of":[11,36,48,63,85,95,114,132,141,148,163,174,182,191],"cellular":[12],"processes.":[13],"Unlike":[14],"water-soluble":[15],"proteins,":[16],"HMPs":[17],"need":[18],"not":[19],"only":[20],"to":[21,30,51,109,134,156],"fold":[22],"but":[23],"also":[24],"get":[25],"inserted":[26],"into":[27],"the":[28,42,57,80,130,158,175,186],"be":[31],"fully":[32],"functional.":[33],"This":[34],"process":[35],"insertion":[38,60,82,138,160],"is":[39,47,199],"mediated":[40],"by":[41,125],"translocon":[43],"complex.":[44],"Thus,":[45],"it":[46],"great":[49],"interest":[50],"develop":[52],"computational":[53,76],"methods":[54],"for":[55,78,103,145,197],"predicting":[56,79],"translocon-mediated":[58],"free":[61,83,101,139,161,177],"energies":[62,84,102,140,162,178],"protein":[64,86,142],"sequences.":[65,87],"RESULT:":[66],"We":[67],"have":[68],"developed":[69],"Membrane":[70],"Insertion":[71],"(MINS),":[72],"novel":[74],"sequence-based":[75],"method":[77],"A":[88,194],"benchmark":[89],"test":[90],"gives":[91],"correlation":[93],"coefficient":[94],"0.74":[96],"between":[97],"predicted":[98,176],"and":[99,188],"observed":[100],"357":[104],"known":[105,169],"cases,":[106],"which":[107],"corresponds":[108],"mean":[111],"unsigned":[112],"error":[113],"0.41":[115],"kcal/mol.":[116],"These":[117],"results":[118],"are":[119],"significantly":[120],"better":[121],"than":[122],"those":[123],"obtained":[124],"traditional":[126],"hydropathy":[127],"analysis.":[128],"Moreover,":[129],"ability":[131],"MINS":[133,153,198],"reasonably":[135],"predict":[136,157],"sequences":[143],"allows":[144],"effective":[146],"identification":[147],"transmembrane":[149],"(TM)":[150],"segments.":[151],"Subsequently,":[152],"was":[154],"applied":[155],"316":[164],"TM":[165],"segments":[166],"found":[167],"structures.":[170],"An":[171],"in-depth":[172],"analysis":[173],"reveals":[179],"number":[181],"interesting":[183],"findings":[184],"about":[185],"biogenesis":[187],"structural":[189],"stability":[190],"HMPs.":[192],"AVAILABILITY:":[193],"web":[195],"server":[196],"available":[200],"at":[201],"http://service.bioinformatik.uni-saarland.de/mins":[202]},"counts_by_year":[{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}