{"id":"https://openalex.org/W2109261827","doi":"https://doi.org/10.1093/nar/gkg532","title":"Static benchmarking of membrane helix predictions","display_name":"Static benchmarking of membrane helix predictions","publication_year":2003,"publication_date":"2003-06-24","ids":{"openalex":"https://openalex.org/W2109261827","doi":"https://doi.org/10.1093/nar/gkg532","mag":"2109261827","pmid":"https://pubmed.ncbi.nlm.nih.gov/12824384"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkg532","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg532","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3642/9487216/gkg532.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","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/nar/article-pdf/31/13/3642/9487216/gkg532.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010395023","display_name":"Andrew Kernytsky","orcid":null},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"A. Kernytsky","raw_affiliation_strings":["CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA. kernytsky@cubic.bioc.columbia.edu","CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, BB217, New York, NY 10032, USA"],"affiliations":[{"raw_affiliation_string":"CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA. kernytsky@cubic.bioc.columbia.edu","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, BB217, New York, NY 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5010395023"],"corresponding_institution_ids":["https://openalex.org/I78577930"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":1.7158,"has_fulltext":true,"cited_by_count":47,"citation_normalized_percentile":{"value":0.83790343,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"31","issue":"13","first_page":"3642","last_page":"3644"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994000196456909,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994000196456909,"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":0.9993000030517578,"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":0.9973999857902527,"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/benchmarking","display_name":"Benchmarking","score":0.7897095680236816},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6535847783088684},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5890936851501465},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.46813735365867615},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4119224548339844},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37296032905578613},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3361554741859436},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33508479595184326},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3289930820465088}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7897095680236816},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6535847783088684},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5890936851501465},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.46813735365867615},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4119224548339844},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37296032905578613},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3361554741859436},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33508479595184326},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3289930820465088},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"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":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkg532","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg532","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3642/9487216/gkg532.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:12824384","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12824384","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.333.3252","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.333.3252","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/31/13/3642.full.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:168939","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:168939","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/168939","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkg532","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg532","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3642/9487216/gkg532.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3497591915","display_name":null,"funder_award_id":"(NIH)","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4474317619","display_name":null,"funder_award_id":"R01-LM07329-01","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G8792241200","display_name":null,"funder_award_id":"R01-LM07329","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2109261827.pdf","grobid_xml":"https://content.openalex.org/works/W2109261827.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W419441076","https://openalex.org/W1526754730","https://openalex.org/W1975304761","https://openalex.org/W2008708467","https://openalex.org/W2018357012","https://openalex.org/W2019187626","https://openalex.org/W2023400093","https://openalex.org/W2026907061","https://openalex.org/W2034410027","https://openalex.org/W2073352736","https://openalex.org/W2074266029","https://openalex.org/W2083268592","https://openalex.org/W2101220662","https://openalex.org/W2114083522","https://openalex.org/W2115840790","https://openalex.org/W2117919289","https://openalex.org/W2122040451","https://openalex.org/W2126405180","https://openalex.org/W2128660550","https://openalex.org/W2130479394","https://openalex.org/W2133549024","https://openalex.org/W2137259082","https://openalex.org/W2144112248","https://openalex.org/W2146396614","https://openalex.org/W2151777569","https://openalex.org/W2153414768","https://openalex.org/W2158906453","https://openalex.org/W2220274965","https://openalex.org/W4255352623"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967","https://openalex.org/W2112883198"],"abstract_inverted_index":{"Prediction":[0],"of":[1,20,41,57,63,76,89,95],"trans-membrane":[2],"helices":[3,125],"continues":[4],"to":[5,48,60,86],"be":[6,106],"a":[7,11],"difficult":[8],"task":[9],"with":[10,126],"few":[12],"prediction":[13,42,50],"methods":[14,70,102],"clearly":[15,23],"taking":[16],"the":[17,37,55,61,77,87,93,120],"lead;":[18],"none":[19],"these":[21],"is":[22,84,135],"best":[24],"on":[25],"all":[26],"accounts.":[27],"Recently,":[28],"we":[29,53,111],"have":[30,45],"carefully":[31],"set":[32],"up":[33],"protocols":[34],"for":[35,117,122,144],"benchmarking":[36],"most":[38,73],"relevant":[39],"aspects":[40],"accuracy":[43,118],"and":[44,114,119],"applied":[46],"it":[47],">30":[49],"methods.":[51],"Here,":[52],"present":[54],"extension":[56],"that":[58,103,136],"analysis":[59],"level":[62],"an":[64],"automatic":[65],"web":[66],"server":[67],"evaluating":[68],"new":[69,82],"(http://cubic.bioc.columbia.edu/services/tmh_benchmark/).":[71],"The":[72],"important":[74],"achievements":[75],"tool":[78],"are:":[79],"(i)":[80],"any":[81,141],"method":[83],"compared":[85],"battery":[88,94],"well-established":[90],"tools;":[91],"(ii)":[92],"measures":[96],"explored":[97],"allows":[98],"spotting":[99],"strengths":[100],"in":[101,147],"may":[104],"not":[105],"'best'":[107],"overall.":[108],"In":[109],"particular,":[110],"report":[112],"per-residue":[113],"per-segment":[115],"scores":[116],"error-rates":[121],"confusing":[123],"membrane":[124,149],"globular":[127],"proteins":[128],"or":[129],"signal":[130],"peptides.":[131],"An":[132],"additional":[133],"feature":[134],"developers":[137],"can":[138],"directly":[139],"investigate":[140],"hydrophobicity":[142],"scale":[143],"its":[145],"potential":[146],"predicting":[148],"helices.":[150]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
