{"id":"https://openalex.org/W2801127413","doi":"https://doi.org/10.1093/database/bay040","title":"AbDb: antibody structure database\u2014a database of PDB-derived antibody structures","display_name":"AbDb: antibody structure database\u2014a database of PDB-derived antibody structures","publication_year":2018,"publication_date":"2018-01-01","ids":{"openalex":"https://openalex.org/W2801127413","doi":"https://doi.org/10.1093/database/bay040","mag":"2801127413","pmid":"https://pubmed.ncbi.nlm.nih.gov/29718130"},"language":"en","primary_location":{"id":"doi:10.1093/database/bay040","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay040","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay040/27438252/bay040.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","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/database/article-pdf/doi/10.1093/database/bay040/27438252/bay040.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075557199","display_name":"Saba Ferdous","orcid":null},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Saba Ferdous","raw_affiliation_strings":["Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065605747","display_name":"Andrew C.R. Martin","orcid":"https://orcid.org/0000-0002-2835-2572"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Andrew C R Martin","raw_affiliation_strings":["Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK"],"raw_orcid":"https://orcid.org/0000-0002-2835-2572","affiliations":[{"raw_affiliation_string":"Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5065605747"],"corresponding_institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1054,"currency":"EUR","value_usd":1136},"fwci":5.5493,"has_fulltext":true,"cited_by_count":101,"citation_normalized_percentile":{"value":0.96582655,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"2018","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11124","display_name":"Protein purification and stability","score":0.9969000220298767,"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/T11157","display_name":"Chronic Lymphocytic Leukemia Research","score":0.9933000206947327,"subfield":{"id":"https://openalex.org/subfields/2716","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.7763193845748901},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5826619267463684},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.5005240440368652},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.50016188621521},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20568779110908508},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1784331500530243},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.06058946251869202},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.05735066533088684}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.7763193845748901},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5826619267463684},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.5005240440368652},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.50016188621521},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20568779110908508},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1784331500530243},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.06058946251869202},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.05735066533088684}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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/database/bay040","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay040","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay040/27438252/bay040.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:29718130","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29718130","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:10046017","is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/10046017/","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":"   Database : the Journal of Biological Databases and Curation       (2018)     (In press).  ","raw_type":"Article"},{"id":"pmh:oai:europepmc.org:4855635","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5925428","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5925428","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5925428","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/bay040","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay040","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay040/27438252/bay040.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2801127413.pdf","grobid_xml":"https://content.openalex.org/works/W2801127413.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1484092314","https://openalex.org/W1969407832","https://openalex.org/W1972352833","https://openalex.org/W1997311863","https://openalex.org/W2009771450","https://openalex.org/W2017956110","https://openalex.org/W2031132894","https://openalex.org/W2037914743","https://openalex.org/W2053844567","https://openalex.org/W2068211846","https://openalex.org/W2074534136","https://openalex.org/W2105185829","https://openalex.org/W2105273832","https://openalex.org/W2106937142","https://openalex.org/W2110505462","https://openalex.org/W2118218075","https://openalex.org/W2122818150","https://openalex.org/W2143467722","https://openalex.org/W2156037313","https://openalex.org/W2165984884","https://openalex.org/W2171049846","https://openalex.org/W2190675974","https://openalex.org/W2509135402","https://openalex.org/W2620998958"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2090630809","https://openalex.org/W2153650863","https://openalex.org/W4246050813","https://openalex.org/W4253991465","https://openalex.org/W2298319713","https://openalex.org/W4387804157","https://openalex.org/W3207853523","https://openalex.org/W3168273531","https://openalex.org/W2589205199"],"abstract_inverted_index":{"In":[0,22],"order":[1],"to":[2,13,188],"analyse":[3],"structures":[4,116,136,146,154,171,191],"of":[5,7,25,31,65,71,88,184,192,204,212],"proteins":[6],"a":[8,29,80,105,108],"particular":[9],"class,":[10],"these":[11],"need":[12,106],"be":[14,46,100,199,222],"extracted":[15],"from":[16,79,134,139,147],"Protein":[17],"Data":[18],"Bank":[19],"(PDB)":[20],"files.":[21],"the":[23,38,62,66,89,131,148,193,202,208,213,218],"case":[24],"antibodies,":[26],"there":[27,103],"are":[28,155,186],"number":[30],"special":[32],"considerations:":[33],"(i)":[34],"identifying":[35],"antibodies":[36,93,185],"in":[37,61,73],"PDB":[39,81,150,205],"is":[40,57,104,163],"not":[41],"trivial,":[42],"(ii)":[43],"they":[44],"may":[45,84,198,221],"crystallized":[47],"with":[48,117,165,172],"or":[49,91,175,207,210,215],"without":[50],"antigen,":[51,216],"(iii)":[52],"for":[53,107],"analysis":[54,70],"purposes,":[55],"one":[56],"normally":[58],"only":[59,173],"interested":[60],"Fv":[63,115,132],"region":[64],"antibody,":[67],"(iv)":[68],"structural":[69],"epitopes,":[72],"particular,":[74],"requires":[75],"individual":[76],"antibody\u2013antigen":[77],"complexes":[78],"file":[82],"which":[83,129,143],"contain":[85],"multiple":[86,153,190],"copies":[87],"same,":[90],"different,":[92],"and":[94,157,159,182,217],"(v)":[95],"standard":[96],"numbering":[97],"schemes":[98],"should":[99],"applied.":[101],"Consequently,":[102],"specialist":[109],"resource":[110],"containing":[111,152],"pre-numbered":[112],"non-redundant":[113],"antibody":[114,135,145,161,214],"their":[118],"cognate":[119],"antigens.":[120],"We":[121],"have":[122,178],"created":[123],"an":[124],"automatically":[125],"updated":[126],"resource,":[127],"AbDb,":[128],"collects":[130],"regions":[133],"using":[137],"information":[138],"our":[140],"SACS":[141],"database":[142],"summarizes":[144],"PDB.":[149],"files":[151],"split":[156],"numbered":[158],"each":[160],"structure":[162],"associated":[164],"its":[166],"antigen":[167],"where":[168],"available.":[169],"Antibody":[170],"light":[174],"heavy":[176],"chains":[177],"also":[179],"been":[180],"processed":[181],"sequences":[183],"compared":[187],"identify":[189],"same":[194],"antibody.":[195],"The":[196],"data":[197],"queried":[200],"on":[201],"basis":[203],"code,":[206],"name":[209],"species":[211],"complete":[219],"datasets":[220],"downloaded.":[223],"Database":[224],"URL:":[225],"www.bioinf.org.uk/abs/abdb/":[226]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":25},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":17},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}
