{"id":"https://openalex.org/W2135416344","doi":"https://doi.org/10.1093/nar/gkj105","title":"The PMDB Protein Model Database","display_name":"The PMDB Protein Model Database","publication_year":2005,"publication_date":"2005-12-28","ids":{"openalex":"https://openalex.org/W2135416344","doi":"https://doi.org/10.1093/nar/gkj105","mag":"2135416344","pmid":"https://pubmed.ncbi.nlm.nih.gov/16381873"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkj105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj105","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D306/3925402/gkj105.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":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","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D306/3925402/gkj105.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086235625","display_name":"Tiziana Castrignan\u00f2","orcid":"https://orcid.org/0000-0002-0689-6720"},"institutions":[{"id":"https://openalex.org/I4210162714","display_name":"Centro Interuniversitario di Ricerca Per lo Sviluppo sostenibile","ror":"https://ror.org/05y8mf384","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210162714"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"T. Castrignano","raw_affiliation_strings":["CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universit\u00e0 e Ricerca. Via dei Tizii, 6/b, I-00185 Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universit\u00e0 e Ricerca. Via dei Tizii, 6/b, I-00185 Rome, Italy","institution_ids":["https://openalex.org/I4210162714"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5086235625"],"corresponding_institution_ids":["https://openalex.org/I4210162714"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.78,"has_fulltext":true,"cited_by_count":305,"citation_normalized_percentile":{"value":0.90559055,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"34","issue":"90001","first_page":"D306","last_page":"D309"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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/T10044","display_name":"Protein Structure and Dynamics","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/T11162","display_name":"Enzyme Structure and Function","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9973000288009644,"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/identifier","display_name":"Identifier","score":0.7574199438095093},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.6236531138420105},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.5943781137466431},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5461814999580383},{"id":"https://openalex.org/keywords/database-model","display_name":"Database model","score":0.5216242074966431},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.47982096672058105},{"id":"https://openalex.org/keywords/database-design","display_name":"Database design","score":0.46078813076019287},{"id":"https://openalex.org/keywords/data-model","display_name":"Data model (GIS)","score":0.44727498292922974},{"id":"https://openalex.org/keywords/download","display_name":"Download","score":0.4282366633415222},{"id":"https://openalex.org/keywords/unique-identifier","display_name":"Unique identifier","score":0.41922807693481445},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40401411056518555},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3276834487915039},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.20998433232307434}],"concepts":[{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.7574199438095093},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6236531138420105},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.5943781137466431},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5461814999580383},{"id":"https://openalex.org/C5968703","wikidata":"https://www.wikidata.org/wiki/Q267136","display_name":"Database model","level":3,"score":0.5216242074966431},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.47982096672058105},{"id":"https://openalex.org/C148840519","wikidata":"https://www.wikidata.org/wiki/Q1049878","display_name":"Database design","level":2,"score":0.46078813076019287},{"id":"https://openalex.org/C100463513","wikidata":"https://www.wikidata.org/wiki/Q5227322","display_name":"Data model (GIS)","level":2,"score":0.44727498292922974},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.4282366633415222},{"id":"https://openalex.org/C119839945","wikidata":"https://www.wikidata.org/wiki/Q6545185","display_name":"Unique identifier","level":3,"score":0.41922807693481445},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40401411056518555},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3276834487915039},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.20998433232307434},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"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/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"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":7,"locations":[{"id":"doi:10.1093/nar/gkj105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj105","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D306/3925402/gkj105.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16381873","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16381873","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:eprints.ucl.ac.uk.OAI2:116236","is_oa":false,"landing_page_url":"http://discovery.ucl.ac.uk/116236/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"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 , 34    D306 - D309.   (2006)      ","raw_type":"Article"},{"id":"pmh:oai:europepmc.org:156908","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1347467","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:iris.uniroma1.it:11573/361599","is_oa":false,"landing_page_url":"http://hdl.handle.net/11573/361599","pdf_url":null,"source":{"id":"https://openalex.org/S4377196107","display_name":"IRIS Research product catalog (Sapienza University of Rome)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1347467","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1347467","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"},{"id":"doi:10.25504/fairsharing.wkaakq","is_oa":true,"landing_page_url":"https://doi.org/10.25504/fairsharing.wkaakq","pdf_url":null,"source":{"id":"https://openalex.org/S7407053452","display_name":"FAIRsharing.org","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"dataset"}],"best_oa_location":{"id":"doi:10.1093/nar/gkj105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj105","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D306/3925402/gkj105.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":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":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.49000000953674316}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2135416344.pdf","grobid_xml":"https://content.openalex.org/works/W2135416344.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W95630632","https://openalex.org/W1511999067","https://openalex.org/W1983747555","https://openalex.org/W1989228404","https://openalex.org/W1989777815","https://openalex.org/W2015461045","https://openalex.org/W2026106250","https://openalex.org/W2026258231","https://openalex.org/W2031704728","https://openalex.org/W2088933990","https://openalex.org/W2096525273","https://openalex.org/W2099875714","https://openalex.org/W2106154817","https://openalex.org/W2125525079","https://openalex.org/W2129253766","https://openalex.org/W2131736388","https://openalex.org/W2135205983","https://openalex.org/W2135416344","https://openalex.org/W2148853951","https://openalex.org/W2154139219","https://openalex.org/W2154733115","https://openalex.org/W2157929322","https://openalex.org/W2158714788","https://openalex.org/W2166458835","https://openalex.org/W2339953814","https://openalex.org/W3200464911","https://openalex.org/W4236324471","https://openalex.org/W4240921265","https://openalex.org/W4241935390","https://openalex.org/W4245803912","https://openalex.org/W4295888250","https://openalex.org/W4390085500"],"related_works":["https://openalex.org/W4248533530","https://openalex.org/W2393499861","https://openalex.org/W2361597612","https://openalex.org/W1045036673","https://openalex.org/W2390897261","https://openalex.org/W2379294600","https://openalex.org/W4297044271","https://openalex.org/W2356642811","https://openalex.org/W296732031","https://openalex.org/W846443833"],"abstract_inverted_index":{"The":[0,18,52],"Protein":[1],"Model":[2],"Database":[3],"(PMDB)":[4],"is":[5,20,38,54,105],"a":[6,39,75,107],"public":[7],"resource":[8],"aimed":[9],"at":[10,56],"storing":[11],"manually":[12],"built":[13],"3D":[14],"models":[15,26,47,63,88],"of":[16,99],"proteins.":[17,51],"database":[19,41,85],"designed":[21],"to":[22,25,61,71,90,96,114],"provide":[23],"access":[24,116],"published":[27],"in":[28,83],"the":[29,84,91,100,117],"scientific":[30],"literature,":[31],"together":[32],"with":[33,65],"validating":[34],"experimental":[35],"data.":[36,118],"It":[37],"relational":[40],"and":[42,58,69,77,86],"it":[43],"currently":[44],"contains":[45],">74,000":[46],"for":[48],"approximately":[49],"240":[50],"system":[53],"accessible":[55],"http://www.caspur.it/PMDB":[57],"allows":[59,111],"predictors":[60],"submit":[62],"along":[64],"related":[66],"supporting":[67],"evidence":[68],"users":[70,113],"download":[72],"them":[73],"through":[74],"simple":[76],"intuitive":[78],"interface.":[79],"Users":[80],"can":[81],"navigate":[82],"retrieve":[87],"referring":[89],"same":[92,101],"target":[93],"protein":[94],"or":[95],"different":[97],"regions":[98],"protein.":[102],"Each":[103],"model":[104],"assigned":[106],"unique":[108],"identifier":[109],"that":[110],"interested":[112],"directly":[115]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":21},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":20},{"year":2019,"cited_by_count":31},{"year":2018,"cited_by_count":28},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":19},{"year":2014,"cited_by_count":19},{"year":2013,"cited_by_count":27},{"year":2012,"cited_by_count":30}],"updated_date":"2026-06-07T08:38:57.713557","created_date":"2016-06-24T00:00:00"}
