{"id":"https://openalex.org/W2056825408","doi":"https://doi.org/10.1093/nar/gkm751","title":"TOPDB: topology data bank of transmembrane proteins","display_name":"TOPDB: topology data bank of transmembrane proteins","publication_year":2007,"publication_date":"2007-10-07","ids":{"openalex":"https://openalex.org/W2056825408","doi":"https://doi.org/10.1093/nar/gkm751","mag":"2056825408","pmid":"https://pubmed.ncbi.nlm.nih.gov/17921502"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkm751","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm751","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_1/D234/7624565/gkm751.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":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/36/suppl_1/D234/7624565/gkm751.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025649527","display_name":"G\u00e1bor Tusn\u00e1dy","orcid":"https://orcid.org/0000-0001-8105-0285"},"institutions":[{"id":"https://openalex.org/I4210151515","display_name":"Institute of Molecular Life Sciences","ror":"https://ror.org/04t4pws42","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210151515","https://openalex.org/I4387152226","https://openalex.org/I80251312"]},{"id":"https://openalex.org/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"government","lineage":["https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"G. E. Tusnady","raw_affiliation_strings":["Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary","institution_ids":["https://openalex.org/I4210151515","https://openalex.org/I7597260"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015278350","display_name":"Lajos Kalm\u00e1r","orcid":"https://orcid.org/0000-0003-3691-8350"},"institutions":[{"id":"https://openalex.org/I4210151515","display_name":"Institute of Molecular Life Sciences","ror":"https://ror.org/04t4pws42","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210151515","https://openalex.org/I4387152226","https://openalex.org/I80251312"]},{"id":"https://openalex.org/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"government","lineage":["https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"L. Kalmar","raw_affiliation_strings":["Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary","institution_ids":["https://openalex.org/I4210151515","https://openalex.org/I7597260"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078144452","display_name":"Istv\u00e1n Simon","orcid":"https://orcid.org/0000-0003-1207-4018"},"institutions":[{"id":"https://openalex.org/I4210151515","display_name":"Institute of Molecular Life Sciences","ror":"https://ror.org/04t4pws42","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210151515","https://openalex.org/I4387152226","https://openalex.org/I80251312"]},{"id":"https://openalex.org/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"government","lineage":["https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"I. Simon","raw_affiliation_strings":["Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary","institution_ids":["https://openalex.org/I4210151515","https://openalex.org/I7597260"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":3.2302,"has_fulltext":true,"cited_by_count":83,"citation_normalized_percentile":{"value":0.92396014,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"Database","first_page":"D234","last_page":"D239"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994999766349792,"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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"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/T12763","display_name":"ATP Synthase and ATPases Research","score":0.9965000152587891,"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-protein","display_name":"Transmembrane protein","score":0.726072371006012},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.6782172322273254},{"id":"https://openalex.org/keywords/membrane-topology","display_name":"Membrane topology","score":0.6558403372764587},{"id":"https://openalex.org/keywords/transmembrane-domain","display_name":"Transmembrane domain","score":0.5917317867279053},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5376144051551819},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.5178561210632324},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5148693323135376},{"id":"https://openalex.org/keywords/membrane-protein","display_name":"Membrane protein","score":0.49538886547088623},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.49465104937553406},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42136719822883606},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4060399532318115},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.348635196685791},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.33569782972335815},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.2936548590660095},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12994876503944397},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12710246443748474},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12276318669319153},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10388994216918945},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.07888105511665344}],"concepts":[{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.726072371006012},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.6782172322273254},{"id":"https://openalex.org/C534586","wikidata":"https://www.wikidata.org/wiki/Q6815143","display_name":"Membrane topology","level":4,"score":0.6558403372764587},{"id":"https://openalex.org/C118892022","wikidata":"https://www.wikidata.org/wiki/Q7834587","display_name":"Transmembrane domain","level":3,"score":0.5917317867279053},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5376144051551819},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.5178561210632324},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5148693323135376},{"id":"https://openalex.org/C144647389","wikidata":"https://www.wikidata.org/wiki/Q423042","display_name":"Membrane protein","level":3,"score":0.49538886547088623},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.49465104937553406},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42136719822883606},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4060399532318115},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.348635196685791},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.33569782972335815},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2936548590660095},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12994876503944397},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12710246443748474},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12276318669319153},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10388994216918945},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.07888105511665344},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"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":"D030562","descriptor_name":"Databases, Protein","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":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkm751","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm751","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_1/D234/7624565/gkm751.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":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:17921502","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17921502","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:pubmedcentral.nih.gov:2238857","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2238857","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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/gkm751","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm751","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_1/D234/7624565/gkm751.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":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320312697","display_name":"Grundy Educational Trust","ror":null},{"id":"https://openalex.org/F4320321994","display_name":"Hungarian Scientific Research Fund","ror":"https://ror.org/00v349e63"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2056825408.pdf","grobid_xml":"https://content.openalex.org/works/W2056825408.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W2019187626","https://openalex.org/W2055043387","https://openalex.org/W2056402029","https://openalex.org/W2061636126","https://openalex.org/W2097775366","https://openalex.org/W2097870001","https://openalex.org/W2111960068","https://openalex.org/W2122040451","https://openalex.org/W2129838159","https://openalex.org/W2130479394","https://openalex.org/W2145020089","https://openalex.org/W2152770371","https://openalex.org/W2153180326","https://openalex.org/W2154081945","https://openalex.org/W2154139219","https://openalex.org/W2158906453","https://openalex.org/W2161062388","https://openalex.org/W2162274915","https://openalex.org/W2163137692","https://openalex.org/W2165724689","https://openalex.org/W4236236547"],"related_works":["https://openalex.org/W2020669016","https://openalex.org/W2088162897","https://openalex.org/W2090630809","https://openalex.org/W4387804157","https://openalex.org/W2106612397","https://openalex.org/W2518314460","https://openalex.org/W2401430279","https://openalex.org/W2119891507","https://openalex.org/W2089869950","https://openalex.org/W2589205199"],"abstract_inverted_index":{"The":[0,144],"Topology":[1],"Data":[2],"Bank":[3],"of":[4,15,51,63,78,147,173,186],"Transmembrane":[5],"Proteins":[6],"(TOPDB)":[7],"is":[8,92,106,164,194],"the":[9,31,39,61,73,99,101,109,117,131,168,171,181],"most":[10,102],"complete":[11],"and":[12,33,86,137,155,180],"comprehensive":[13],"collection":[14,77],"transmembrane":[16,46,65,119,174,191],"protein":[17,97,133],"datasets":[18],"containing":[19],"experimentally":[20,187],"derived":[21],"topology":[22,62,90,104,120,184],"information":[23,28,91,129,185],"currently":[24],"available.":[25],"It":[26],"contains":[27,128],"gathered":[29],"from":[30,34,72,84,87],"literature":[32],"public":[35],"databases":[36,179],"available":[37,176,195],"on":[38,130],"internet":[40],"for":[41,95,151,161],"more":[42],"than":[43],"a":[44],"thousand":[45],"proteins.":[47,66,192],"TOPDB":[48,126,148,163,193],"collects":[49],"details":[50],"various":[52,141],"experiments":[53],"that":[54,105],"were":[55],"carried":[56],"out":[57],"to":[58,69,140,166],"learn":[59],"about":[60],"particular":[64],"In":[67],"addition":[68],"experimental":[70,111],"data":[71,80,156],"literature,":[74],"an":[75],"extensive":[76],"structural":[79],"was":[81,113],"also":[82,114,127],"compiled":[83],"PDB":[85],"PDBTM.":[88],"Because":[89],"often":[93],"incomplete,":[94],"each":[96],"in":[98,125,177],"database":[100],"probable":[103],"consistent":[107],"with":[108],"collected":[110],"constraints":[112],"calculated":[115],"using":[116],"HMMTOP":[118],"prediction":[121],"algorithm.":[122],"Each":[123],"record":[124],"given":[132],"sequence,":[134],"name,":[135],"organism":[136],"cross":[138],"references":[139],"other":[142],"databases.":[143],"web":[145],"interface":[146],"includes":[149],"tools":[150],"searching,":[152],"relational":[153],"querying":[154],"browsing":[157],"as":[158,160],"well":[159],"visualization.":[162],"designed":[165],"bridge":[167],"gap":[169],"between":[170],"number":[172],"proteins":[175],"sequence":[178],"publicly":[182],"accessible":[183],"or":[188],"computationally":[189],"studied":[190],"at":[196],"http://topdb.enzim.hu.":[197]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":5}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
