{"id":"https://openalex.org/W2512372054","doi":"https://doi.org/10.1093/bioinformatics/btw514","title":"PRODIGY: a web server for predicting the binding affinity of protein\u2013protein complexes","display_name":"PRODIGY: a web server for predicting the binding affinity of protein\u2013protein complexes","publication_year":2016,"publication_date":"2016-08-08","ids":{"openalex":"https://openalex.org/W2512372054","doi":"https://doi.org/10.1093/bioinformatics/btw514","mag":"2512372054","pmid":"https://pubmed.ncbi.nlm.nih.gov/27503228"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw514","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw514","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/23/3676/13618823/btw514.pdf","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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/23/3676/13618823/btw514.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086880868","display_name":"Li C. Xue","orcid":"https://orcid.org/0000-0002-2613-538X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Li C. Xue","raw_affiliation_strings":["Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science - Department of Chemistry, Utrecht University, 3584CH Utrecht, The Netherlands","Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA;"],"affiliations":[{"raw_affiliation_string":"Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science - Department of Chemistry, Utrecht University, 3584CH Utrecht, The Netherlands","institution_ids":[]},{"raw_affiliation_string":"Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA;","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044499597","display_name":"Jo\u00e3o Rodrigues","orcid":"https://orcid.org/0000-0001-9796-3193"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o Pglm Rodrigues","raw_affiliation_strings":["Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science - Department of Chemistry, Utrecht University, 3584CH Utrecht, The Netherlands","Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Sci-ence -Chemistry, Utrecht University, Utrecht, The Netherlands. AB"],"affiliations":[{"raw_affiliation_string":"Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science - Department of Chemistry, Utrecht University, 3584CH Utrecht, The Netherlands","institution_ids":[]},{"raw_affiliation_string":"Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Sci-ence -Chemistry, Utrecht University, Utrecht, The Netherlands. AB","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023101546","display_name":"Panagiotis L. Kastritis","orcid":"https://orcid.org/0000-0002-1463-8422"},"institutions":[{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]},{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["DE","NL"],"is_corresponding":false,"raw_author_name":"Panagiotis L. Kastritis","raw_affiliation_strings":["Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science - Department of Chemistry, Utrecht University, 3584CH Utrecht, The Netherlands","Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Sci-ence -Chemistry, Utrecht University, Utrecht, The Netherlands. AB",": European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science - Department of Chemistry, Utrecht University, 3584CH Utrecht, The Netherlands","institution_ids":[]},{"raw_affiliation_string":"Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Sci-ence -Chemistry, Utrecht University, Utrecht, The Netherlands. AB","institution_ids":["https://openalex.org/I193662353"]},{"raw_affiliation_string":": European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany","institution_ids":["https://openalex.org/I4210153543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064072429","display_name":"Alexandre M. J. J. Bonvin","orcid":"https://orcid.org/0000-0001-7369-1322"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Alexandre Mjj Bonvin","raw_affiliation_strings":["Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science - Department of Chemistry, Utrecht University, 3584CH Utrecht, The Netherlands","Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Sci-ence -Chemistry, Utrecht University, Utrecht, The Netherlands. AB"],"affiliations":[{"raw_affiliation_string":"Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science - Department of Chemistry, Utrecht University, 3584CH Utrecht, The Netherlands","institution_ids":[]},{"raw_affiliation_string":"Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Sci-ence -Chemistry, Utrecht University, Utrecht, The Netherlands. AB","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086878755","display_name":"Anna Vangone","orcid":"https://orcid.org/0000-0003-2485-7378"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Anna Vangone","raw_affiliation_strings":["Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science - Department of Chemistry, Utrecht University, 3584CH Utrecht, The Netherlands","Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Sci-ence -Chemistry, Utrecht University, Utrecht, The Netherlands. AB"],"affiliations":[{"raw_affiliation_string":"Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science - Department of Chemistry, Utrecht University, 3584CH Utrecht, The Netherlands","institution_ids":[]},{"raw_affiliation_string":"Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Sci-ence -Chemistry, Utrecht University, Utrecht, The Netherlands. AB","institution_ids":["https://openalex.org/I193662353"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5086880868"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":15.1661,"has_fulltext":false,"cited_by_count":1361,"citation_normalized_percentile":{"value":0.9927507,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"32","issue":"23","first_page":"3676","last_page":"3678"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9959999918937683,"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/web-server","display_name":"Web server","score":0.6251934170722961},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5197665095329285},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.47017329931259155},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.43458855152130127},{"id":"https://openalex.org/keywords/binding-protein","display_name":"Binding protein","score":0.41318970918655396},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3634421229362488},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.30545228719711304},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30381330847740173},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2972288727760315},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.23243024945259094},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.16930967569351196},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1684975028038025},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1513153612613678}],"concepts":[{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6251934170722961},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5197665095329285},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.47017329931259155},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.43458855152130127},{"id":"https://openalex.org/C553089730","wikidata":"https://www.wikidata.org/wiki/Q4914021","display_name":"Binding protein","level":3,"score":0.41318970918655396},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3634421229362488},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.30545228719711304},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30381330847740173},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2972288727760315},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.23243024945259094},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.16930967569351196},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1684975028038025},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1513153612613678},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"D011487","descriptor_name":"Protein Conformation","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw514","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw514","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/23/3676/13618823/btw514.pdf","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:27503228","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27503228","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:uu:oai:dspace.library.uu.nl:1874/345622","is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/345622","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 32(23), 3676. Oxford University Press","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw514","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw514","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/23/3676/13618823/btw514.pdf","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"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.7099999785423279,"id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G5109729550","display_name":null,"funder_award_id":"722.014.005","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2512372054.pdf","grobid_xml":"https://content.openalex.org/works/W2512372054.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1882636497","https://openalex.org/W1915490970","https://openalex.org/W1948562438","https://openalex.org/W1997803213","https://openalex.org/W2010612779","https://openalex.org/W2036309115","https://openalex.org/W2110720709","https://openalex.org/W2110869427","https://openalex.org/W2114027069","https://openalex.org/W2123375001","https://openalex.org/W2129562311","https://openalex.org/W2132625528","https://openalex.org/W2140875146","https://openalex.org/W2157733131","https://openalex.org/W2165948287","https://openalex.org/W2253581743","https://openalex.org/W2342374505","https://openalex.org/W6704437023"],"related_works":["https://openalex.org/W2378005410","https://openalex.org/W2099982459","https://openalex.org/W2109298101","https://openalex.org/W2007507741","https://openalex.org/W2159860826","https://openalex.org/W3192210502","https://openalex.org/W1981737222","https://openalex.org/W1569394480","https://openalex.org/W4390876228","https://openalex.org/W1998222399"],"abstract_inverted_index":{"PRODIGY":[0],"is":[1],"freely":[2],"available":[3],"at:":[4],"http://milou.science.uu.nl/services/PRODIGY":[5],"CONTACT:":[6],"a.m.j.j.bonvin@uu.nl,":[7],"a.vangone@uu.nl.":[8]},"counts_by_year":[{"year":2026,"cited_by_count":85},{"year":2025,"cited_by_count":257},{"year":2024,"cited_by_count":223},{"year":2023,"cited_by_count":207},{"year":2022,"cited_by_count":208},{"year":2021,"cited_by_count":162},{"year":2020,"cited_by_count":131},{"year":2019,"cited_by_count":43},{"year":2018,"cited_by_count":24},{"year":2017,"cited_by_count":17},{"year":2016,"cited_by_count":3}],"updated_date":"2026-04-17T18:11:37.981687","created_date":"2025-10-10T00:00:00"}