{"id":"https://openalex.org/W1998643444","doi":"https://doi.org/10.1093/nar/gkj039","title":"AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB","display_name":"AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB","publication_year":2005,"publication_date":"2005-12-28","ids":{"openalex":"https://openalex.org/W1998643444","doi":"https://doi.org/10.1093/nar/gkj039","mag":"1998643444","pmid":"https://pubmed.ncbi.nlm.nih.gov/16381925"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkj039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj039","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D522/3924244/gkj039.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":"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":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D522/3924244/gkj039.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018855544","display_name":"Peter C. Block","orcid":"https://orcid.org/0000-0002-7939-2849"},"institutions":[{"id":"https://openalex.org/I161103922","display_name":"Philipps University of Marburg","ror":"https://ror.org/01rdrb571","country_code":"DE","type":"education","lineage":["https://openalex.org/I161103922"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"P. Block","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany","institution_ids":["https://openalex.org/I161103922"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5018855544"],"corresponding_institution_ids":["https://openalex.org/I161103922"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.5319,"has_fulltext":true,"cited_by_count":89,"citation_normalized_percentile":{"value":0.88919316,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"34","issue":"90001","first_page":"D522","last_page":"D526"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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/T10044","display_name":"Protein Structure and Dynamics","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/T11162","display_name":"Enzyme Structure and Function","score":0.9975000023841858,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9958999752998352,"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":0.9470791220664978},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.7843633890151978},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.7344377040863037},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.6006484627723694},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5377281904220581},{"id":"https://openalex.org/keywords/value","display_name":"Value (mathematics)","score":0.5149027109146118},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49791765213012695},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.4401400089263916},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4092337191104889},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3748389780521393},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3512069880962372},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3081730008125305},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.23166483640670776}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.9470791220664978},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.7843633890151978},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.7344377040863037},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6006484627723694},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5377281904220581},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.5149027109146118},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49791765213012695},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.4401400089263916},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4092337191104889},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3748389780521393},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3512069880962372},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3081730008125305},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.23166483640670776},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","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":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"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":6,"locations":[{"id":"doi:10.1093/nar/gkj039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj039","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D522/3924244/gkj039.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":"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:16381925","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16381925","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:10.1.1.276.3146","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.276.3146","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/b4/d9/Nucleic_Acids_Res_2006_Jan_1_34(Database_issue)_D522-D526.tar.gz","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.580.5606","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.580.5606","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/34/suppl_1/D522.full-text-lowres.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:156864","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1347402","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:1347402","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1347402","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/gkj039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj039","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D522/3924244/gkj039.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":"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":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1998643444.pdf","grobid_xml":"https://content.openalex.org/works/W1998643444.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1505394602","https://openalex.org/W1605578858","https://openalex.org/W1656114533","https://openalex.org/W1875906722","https://openalex.org/W1975147762","https://openalex.org/W1993046136","https://openalex.org/W2003117865","https://openalex.org/W2014123957","https://openalex.org/W2038147869","https://openalex.org/W2040617462","https://openalex.org/W2051993924","https://openalex.org/W2054668663","https://openalex.org/W2062663912","https://openalex.org/W2069471410","https://openalex.org/W2085277871","https://openalex.org/W2089035939","https://openalex.org/W2091379422","https://openalex.org/W2092285329","https://openalex.org/W2098622919","https://openalex.org/W2102839822","https://openalex.org/W2111078532","https://openalex.org/W2120138074","https://openalex.org/W2124850224","https://openalex.org/W2128332459","https://openalex.org/W2129748900","https://openalex.org/W2130479394","https://openalex.org/W2138473864","https://openalex.org/W2140571075","https://openalex.org/W2143567718","https://openalex.org/W2146465875"],"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/W4387033830","https://openalex.org/W3013529667","https://openalex.org/W2769925250"],"abstract_inverted_index":{"AffinDB":[0,55,112],"is":[1,19,156],"a":[2,160],"database":[3,155],"of":[4,41,85,102,123,130,172],"affinity":[5,42,50,60,71,87,124],"data":[6,25,78,138,177],"for":[7,163,174,182],"structurally":[8],"resolved":[9],"protein-ligand":[10,67],"complexes":[11],"from":[12,28,33,45],"the":[13,29,37,70,82,86,92,103,131,170],"Protein":[14],"Data":[15],"Bank":[16],"(PDB).":[17],"It":[18],"freely":[20],"accessible":[21],"at":[22],"http://www.agklebe.de/affinity.":[23],"Affinity":[24],"are":[26,79],"collected":[27],"scientific":[30],"literature,":[31],"both":[32],"primary":[34],"sources":[35],"describing":[36],"original":[38],"experimental":[39,83],"work":[40],"determination":[43],"and":[44,76,99,109,127,136,141,169],"secondary":[46],"references":[47],"which":[48],"report":[49],"values":[51],"determined":[52],"by":[53,116,120],"others.":[54],"currently":[56],"contains":[57],"over":[58],"730":[59],"entries":[61],"covering":[62],"more":[63],"than":[64],"450":[65],"different":[66],"complexes.":[68],"Besides":[69],"value,":[72],"PDB":[73,117],"summary":[74],"information":[75],"additional":[77],"provided,":[80],"including":[81],"conditions":[84],"measurement":[88],"(if":[89],"available":[90],"in":[91,151,166,184],"corresponding":[93],"reference);":[94],"2D":[95],"drawing,":[96],"SMILES":[97],"code":[98,118],"molecular":[100,134],"weight":[101],"ligand;":[104],"links":[105],"to":[106,158],"other":[107],"databases,":[108],"bibliographic":[110],"information.":[111],"can":[113,145],"be":[114,146,159],"queried":[115],"or":[119],"any":[121],"combination":[122],"range,":[125],"temperature":[126],"pH":[128],"value":[129],"measurement,":[132],"ligand":[133],"weight,":[135],"publication":[137],"(author,":[139],"journal":[140],"year).":[142],"Search":[143],"results":[144],"saved":[147],"as":[148,180],"tabular":[149],"reports":[150],"text":[152],"files.":[153],"The":[154],"supposed":[157],"valuable":[161],"resource":[162],"researchers":[164],"interested":[165],"biomolecular":[167],"recognition":[168],"development":[171],"tools":[173],"correlating":[175],"structural":[176],"with":[178],"affinities,":[179],"needed,":[181],"example,":[183],"structure-based":[185],"drug":[186],"design.":[187]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":5}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
