{"id":"https://openalex.org/W2056402029","doi":"https://doi.org/10.1093/nar/gki002","title":"PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank","display_name":"PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank","publication_year":2004,"publication_date":"2004-12-17","ids":{"openalex":"https://openalex.org/W2056402029","doi":"https://doi.org/10.1093/nar/gki002","mag":"2056402029","pmid":"https://pubmed.ncbi.nlm.nih.gov/15608195"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki002","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki002","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D275/7621380/gki002.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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":"hybrid","oa_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D275/7621380/gki002.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/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"funder","lineage":["https://openalex.org/I7597260"]},{"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"]}],"countries":["HU"],"is_corresponding":true,"raw_author_name":"G. E. Tusnady","raw_affiliation_strings":["Institute of Enzymology, BRC, Hungarian Academy of Sciences, H-1518 Budapest, P.O. Box 7, Hungary"],"affiliations":[{"raw_affiliation_string":"Institute of Enzymology, BRC, Hungarian Academy of Sciences, H-1518 Budapest, P.O. Box 7, Hungary","institution_ids":["https://openalex.org/I4210151515","https://openalex.org/I7597260"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5025649527"],"corresponding_institution_ids":["https://openalex.org/I4210151515","https://openalex.org/I7597260"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":3.0146,"has_fulltext":true,"cited_by_count":274,"citation_normalized_percentile":{"value":0.91428325,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"33","issue":"Database issue","first_page":"D275","last_page":"D278"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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":0.9980999827384949,"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":0.9980000257492065,"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/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.9700353741645813},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.8161144852638245},{"id":"https://openalex.org/keywords/transmembrane-protein","display_name":"Transmembrane protein","score":0.6659167408943176},{"id":"https://openalex.org/keywords/membrane-protein","display_name":"Membrane protein","score":0.596752405166626},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.565854549407959},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3706439733505249},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.37017738819122314},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.35127323865890503},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.273567795753479},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2704205811023712},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.16645216941833496}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.9700353741645813},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.8161144852638245},{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.6659167408943176},{"id":"https://openalex.org/C144647389","wikidata":"https://www.wikidata.org/wiki/Q423042","display_name":"Membrane protein","level":3,"score":0.596752405166626},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.565854549407959},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3706439733505249},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.37017738819122314},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.35127323865890503},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.273567795753479},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2704205811023712},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.16645216941833496},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"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":5,"locations":[{"id":"doi:10.1093/nar/gki002","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki002","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D275/7621380/gki002.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15608195","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15608195","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:10.1.1.98.674","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.98.674","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.enzim.hu/~tusi/papers/NAR_33_D275(2005).pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:163470","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC539956","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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:539956","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/539956","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/gki002","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki002","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D275/7621380/gki002.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2056402029.pdf","grobid_xml":"https://content.openalex.org/works/W2056402029.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1947778485","https://openalex.org/W2008708467","https://openalex.org/W2041488448","https://openalex.org/W2113442468","https://openalex.org/W2129838159","https://openalex.org/W2130479394","https://openalex.org/W2148853951","https://openalex.org/W2152770371","https://openalex.org/W2163137692","https://openalex.org/W2165724689","https://openalex.org/W6603112357"],"related_works":["https://openalex.org/W3126783617","https://openalex.org/W2732388178","https://openalex.org/W3093468851","https://openalex.org/W4353055924","https://openalex.org/W2806488847","https://openalex.org/W2121688928","https://openalex.org/W2772651271","https://openalex.org/W4389958586","https://openalex.org/W2769925250","https://openalex.org/W4361279638"],"abstract_inverted_index":{"PDB_TM":[0,78,85,102],"is":[1,104],"a":[2],"database":[3,24,86,103],"for":[4],"transmembrane":[5,15,59],"proteins":[6,16],"with":[7,96],"known":[8],"structures.":[9],"It":[10],"aims":[11],"to":[12,27,45,56,67],"collect":[13],"all":[14,68],"that":[17],"are":[18,34],"deposited":[19],"in":[20,76],"the":[21,37,47,52,72,77,84,97],"protein":[22],"structure":[23],"(PDB)":[25],"and":[26,55,60,71],"determine":[28],"their":[29],"membrane-spanning":[30],"regions.":[31],"These":[32],"assignments":[33],"based":[35],"on":[36],"TMDET":[38,82],"algorithm,":[39,83],"which":[40],"uses":[41],"only":[42],"structural":[43],"information":[44],"locate":[46],"most":[48],"likely":[49],"position":[50],"of":[51],"lipid":[53],"bilayer":[54],"distinguish":[57],"between":[58],"globular":[61],"proteins.":[62],"This":[63],"algorithm":[64],"was":[65],"applied":[66],"PDB":[69,99],"entries":[70],"results":[73],"were":[74],"collected":[75],"database.":[79],"By":[80],"using":[81],"can":[87],"be":[88],"automatically":[89],"updated":[90],"every":[91],"week,":[92],"keeping":[93],"it":[94],"synchronized":[95],"latest":[98],"updates.":[100],"The":[101],"available":[105],"at":[106],"http://www.enzim.hu/PDB_TM.":[107]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":13},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":18},{"year":2014,"cited_by_count":18},{"year":2013,"cited_by_count":35},{"year":2012,"cited_by_count":22}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
