{"id":"https://openalex.org/W2919319795","doi":"https://doi.org/10.1093/bioinformatics/btz143","title":"Aggrescan3D standalone package for structure-based prediction of protein aggregation properties","display_name":"Aggrescan3D standalone package for structure-based prediction of protein aggregation properties","publication_year":2019,"publication_date":"2019-02-27","ids":{"openalex":"https://openalex.org/W2919319795","doi":"https://doi.org/10.1093/bioinformatics/btz143","mag":"2919319795","pmid":"https://pubmed.ncbi.nlm.nih.gov/30825368"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz143","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz143","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","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 Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002785720","display_name":"Valent\u00edn Iglesias","orcid":"https://orcid.org/0000-0002-6133-0869"},"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":"Valentin Iglesias","raw_affiliation_strings":["Institut de Biotecnologia i de Biomedicina and Departament de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut de Biotecnologia i de Biomedicina and Departament de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023082406","display_name":"Mateusz Kurci\u0144ski","orcid":"https://orcid.org/0000-0002-5385-2069"},"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":"Mateusz Kurcinski","raw_affiliation_strings":["Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"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 and Departament de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut de Biotecnologia i de Biomedicina and Departament de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona, 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 Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0001-7623-0935","affiliations":[{"raw_affiliation_string":"Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"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":1.3666,"has_fulltext":false,"cited_by_count":37,"citation_normalized_percentile":{"value":0.8063135,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"35","issue":"19","first_page":"3834","last_page":"3835"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11124","display_name":"Protein purification and stability","score":0.5005000233650208,"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/T11124","display_name":"Protein purification and stability","score":0.5005000233650208,"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":0.19830000400543213,"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":0.10589999705553055,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.8245576620101929},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7031391263008118},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.5101225972175598},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4125620722770691},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3848263621330261},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.36967170238494873},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33151212334632874},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.24446234107017517},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.21758762001991272},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.12345045804977417}],"concepts":[{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.8245576620101929},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7031391263008118},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.5101225972175598},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4125620722770691},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3848263621330261},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.36967170238494873},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33151212334632874},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.24446234107017517},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.21758762001991272},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.12345045804977417},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D066329","descriptor_name":"Protein Aggregates","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066329","descriptor_name":"Protein Aggregates","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066329","descriptor_name":"Protein Aggregates","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz143","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz143","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:30825368","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30825368","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4842262021","display_name":null,"funder_award_id":"BIO2016\u201378,310-R","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"}],"funders":[{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W2001090783","https://openalex.org/W2023490488","https://openalex.org/W2059093611","https://openalex.org/W2074726906","https://openalex.org/W2103083136","https://openalex.org/W2133425057","https://openalex.org/W2253581743","https://openalex.org/W2396317614","https://openalex.org/W2411303265","https://openalex.org/W2788217325","https://openalex.org/W2788954552","https://openalex.org/W2883869520","https://openalex.org/W2886024678","https://openalex.org/W2896148359","https://openalex.org/W3099088600"],"related_works":["https://openalex.org/W4389426664","https://openalex.org/W3008797681","https://openalex.org/W2566205467","https://openalex.org/W3012616639","https://openalex.org/W3126000805","https://openalex.org/W3198565742","https://openalex.org/W2010064959","https://openalex.org/W2157390150","https://openalex.org/W2119742499","https://openalex.org/W1985266044"],"abstract_inverted_index":{"SUMMARY:":[0],"Aggrescan3D":[1],"(A3D)":[2],"standalone":[3,59,99,121,144],"is":[4,62,100,107,115],"a":[5,40,72,84],"multiplatform":[6],"Python":[7],"package":[8],"for":[9,88,109,134],"structure-based":[10],"prediction":[11],"of":[12,19,26,50,65,74,79,129],"protein":[13,20,27,51],"aggregation":[14,32,56],"properties":[15],"and":[16,34,82,111,127,131,137],"rational":[17],"design":[18],"solubility.":[21],"A3D":[22,60,98,120,143],"allows":[23],"the":[24,48,55,66,103,142],"re-design":[25],"solubility":[28],"by":[29,39],"combining":[30],"structural":[31],"propensity":[33],"stability":[35],"predictions,":[36],"as":[37],"demonstrated":[38],"recent":[41],"experimental":[42],"study.":[43],"It":[44,114],"also":[45],"enables":[46],"predicting":[47],"impact":[49],"conformational":[52],"fluctuations":[53],"on":[54],"properties.":[57],"The":[58,119],"version":[61],"an":[63],"upgrade":[64],"original":[67],"web":[68],"server":[69],"implementation-it":[70],"introduces":[71],"number":[73],"customizable":[75],"options,":[76],"automated":[77],"analysis":[78],"multiple":[80],"mutations":[81],"offers":[83],"flexible":[85],"computational":[86,93],"framework":[87],"merging":[89],"it":[90],"with":[91,125],"other":[92],"tools.":[94],"AVAILABILITY":[95],"AND":[96],"IMPLEMENTATION:":[97],"distributed":[101],"under":[102],"MIT":[104],"license,":[105],"which":[106],"free":[108],"academic":[110],"non-profit":[112],"users.":[113],"implemented":[116],"in":[117,141],"Python.":[118],"source":[122],"code,":[123],"wiki":[124],"documentation":[126],"examples":[128],"use,":[130],"installation":[132],"instructions":[133],"Linux,":[135],"macOS":[136],"Windows":[138],"are":[139],"available":[140],"repository":[145],"at":[146],"https://bitbucket.org/lcbio/aggrescan3d.":[147]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
