{"id":"https://openalex.org/W4224254952","doi":"https://doi.org/10.1093/bioinformatics/btac215","title":"A3D database: structure-based predictions of protein aggregation for the human proteome","display_name":"A3D database: structure-based predictions of protein aggregation for the human proteome","publication_year":2022,"publication_date":"2022-04-19","ids":{"openalex":"https://openalex.org/W4224254952","doi":"https://doi.org/10.1093/bioinformatics/btac215","pmid":"https://pubmed.ncbi.nlm.nih.gov/35445695"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac215","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac215","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9746890","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036112045","display_name":"Aleksandra E. Badaczewska-Dawid","orcid":"https://orcid.org/0000-0003-1832-4364"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aleksandra E Badaczewska-Dawid","raw_affiliation_strings":["Department of Chemistry, Iowa State University , Ames, 50011 IA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Iowa State University , Ames, 50011 IA, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053487672","display_name":"Javier Garc\u00eda\u2010Pardo","orcid":"https://orcid.org/0000-0001-9179-6371"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Javier Garcia-Pardo","raw_affiliation_strings":["Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona , 08193 Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona , 08193 Barcelona, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078317077","display_name":"Aleksander Kuriata","orcid":null},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Aleksander Kuriata","raw_affiliation_strings":["Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw , Warsaw 02-093, Poland"],"affiliations":[{"raw_affiliation_string":"Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw , Warsaw 02-093, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071263053","display_name":"Jordi Pujols","orcid":"https://orcid.org/0000-0001-9424-5866"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jordi Pujols","raw_affiliation_strings":["Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona , 08193 Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona , 08193 Barcelona, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025858582","display_name":"Salvador Ventura","orcid":"https://orcid.org/0000-0002-9652-6351"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Salvador Ventura","raw_affiliation_strings":["Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona , 08193 Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona , 08193 Barcelona, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006850152","display_name":"Sebastian Kmiecik","orcid":"https://orcid.org/0000-0001-7623-0935"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Sebastian Kmiecik","raw_affiliation_strings":["Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw , Warsaw 02-093, Poland"],"affiliations":[{"raw_affiliation_string":"Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw , Warsaw 02-093, Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5006850152","https://openalex.org/A5025858582"],"corresponding_institution_ids":["https://openalex.org/I123044942","https://openalex.org/I4654613"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9533,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.72574956,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"11","first_page":"3121","last_page":"3123"},"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":0.9966999888420105,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9959999918937683,"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/uniprot","display_name":"UniProt","score":0.7256858348846436},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6910285949707031},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5262724161148071},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.44077038764953613},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.4270758330821991},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.42011022567749023},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32085248827934265},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.284712553024292},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.19653373956680298},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13396933674812317},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.09971317648887634}],"concepts":[{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.7256858348846436},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6910285949707031},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5262724161148071},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.44077038764953613},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.4270758330821991},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.42011022567749023},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32085248827934265},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.284712553024292},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.19653373956680298},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13396933674812317},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.09971317648887634},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012995","descriptor_name":"Solubility","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012995","descriptor_name":"Solubility","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012995","descriptor_name":"Solubility","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066329","descriptor_name":"Protein Aggregates","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066329","descriptor_name":"Protein Aggregates","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066329","descriptor_name":"Protein Aggregates","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btac215","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac215","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35445695","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35445695","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9746890","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9746890","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:zenodo.org:8344288","is_oa":true,"landing_page_url":"https://zenodo.org/record/8344288","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9746890","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9746890","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3581538381","display_name":null,"funder_award_id":"2020/39/B/NZ2/01301","funder_id":"https://openalex.org/F4320322650","funder_display_name":"Narodowym Centrum Nauki"},{"id":"https://openalex.org/G4270421355","display_name":null,"funder_award_id":"PID2019-105017RB-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G49740995","display_name":null,"funder_award_id":"PhasAge/H2020-WIDESPREAD-2020-5","funder_id":"https://openalex.org/F4320316317","funder_display_name":"Xi'an Eurasia University"}],"funders":[{"id":"https://openalex.org/F4320316317","display_name":"Xi'an Eurasia University","ror":null},{"id":"https://openalex.org/F4320322650","display_name":"Narodowym Centrum Nauki","ror":"https://ror.org/03ha2q922"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W2074726906","https://openalex.org/W2795330179","https://openalex.org/W2883869520","https://openalex.org/W2919319795","https://openalex.org/W2943407516","https://openalex.org/W2967131843","https://openalex.org/W3024233049","https://openalex.org/W3105706706","https://openalex.org/W3124832172","https://openalex.org/W3177437504","https://openalex.org/W3177828909","https://openalex.org/W3180046090","https://openalex.org/W3183475563"],"related_works":["https://openalex.org/W2288906059","https://openalex.org/W4376862128","https://openalex.org/W4296966554","https://openalex.org/W2030530458","https://openalex.org/W2546159719","https://openalex.org/W2296132555","https://openalex.org/W2118200955","https://openalex.org/W2103435205","https://openalex.org/W2093730890","https://openalex.org/W2131736388"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
