{"id":"https://openalex.org/W2031616673","doi":"https://doi.org/10.1093/nar/gkt887","title":"3did: a catalog of domain-based interactions of known three-dimensional structure","display_name":"3did: a catalog of domain-based interactions of known three-dimensional structure","publication_year":2013,"publication_date":"2013-09-29","ids":{"openalex":"https://openalex.org/W2031616673","doi":"https://doi.org/10.1093/nar/gkt887","mag":"2031616673","pmid":"https://pubmed.ncbi.nlm.nih.gov/24081580"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkt887","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt887","pdf_url":"https://academic.oup.com/nar/article-pdf/42/D1/D374/3670559/gkt887.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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/42/D1/D374/3670559/gkt887.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013423377","display_name":"Roberto Mosca","orcid":"https://orcid.org/0000-0002-3244-1885"},"institutions":[{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Roberto Mosca","raw_affiliation_strings":["Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain, Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy, California Institute for Quantitative Biomedical Research (qb3) and Department of Bioengineering and Therapeutic Sciences, MC 2530, University of California San Francisco (UCSF) CA 94158-2330, USA and Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, 08010 Barcelona, Spain","Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain, Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy, California Institute for Quantitative Biomedical Research (qb3) and Department of Bioengineering and Therapeutic Sciences, MC 2530, University of California San Francisco (UCSF) CA 94158-2330, USA and Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, 08010 Barcelona, Spain","institution_ids":[]},{"raw_affiliation_string":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats, Barcelona, Spain","institution_ids":["https://openalex.org/I11932220"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005880496","display_name":"Arnaud C\u00e9ol","orcid":"https://orcid.org/0000-0001-9533-4246"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]},{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]},{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]},{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["ES","IT","US"],"is_corresponding":false,"raw_author_name":"Arnaud C\u00e9ol","raw_affiliation_strings":["Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain, 2Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy, 3California Institute for Quantitative Biomedical Research (qb3) and Department of Bioengineering and Therapeutic Sciences, MC 2530, University of California San Francisco (UCSF) CA 94158\u20132330, USA and 4Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, 08010 Barcelona, Spain","Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain, 2Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy, 3California Institute for Quantitative Biomedical Research (qb3) and Department of Bioengineering and Therapeutic Sciences, MC 2530, University of California San Francisco (UCSF) CA 94158\u20132330, USA and 4Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, 08010 Barcelona, Spain","institution_ids":["https://openalex.org/I4210151238","https://openalex.org/I4210122345","https://openalex.org/I180670191","https://openalex.org/I9617848","https://openalex.org/I11932220","https://openalex.org/I30771326"]},{"raw_affiliation_string":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats, Barcelona, Spain","institution_ids":["https://openalex.org/I11932220"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032625918","display_name":"Amelie Stein","orcid":"https://orcid.org/0000-0002-5862-1681"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]},{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]},{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]}],"countries":["ES","IT","US"],"is_corresponding":false,"raw_author_name":"Amelie Stein","raw_affiliation_strings":["Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain, 2Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy, 3California Institute for Quantitative Biomedical Research (qb3) and Department of Bioengineering and Therapeutic Sciences, MC 2530, University of California San Francisco (UCSF) CA 94158\u20132330, USA and 4Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, 08010 Barcelona, Spain","Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain, 2Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy, 3California Institute for Quantitative Biomedical Research (qb3) and Department of Bioengineering and Therapeutic Sciences, MC 2530, University of California San Francisco (UCSF) CA 94158\u20132330, USA and 4Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, 08010 Barcelona, Spain","institution_ids":["https://openalex.org/I4210151238","https://openalex.org/I4210122345","https://openalex.org/I180670191","https://openalex.org/I9617848","https://openalex.org/I11932220","https://openalex.org/I30771326"]},{"raw_affiliation_string":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats, Barcelona, Spain","institution_ids":["https://openalex.org/I11932220"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080709112","display_name":"Roger Olivella","orcid":"https://orcid.org/0000-0001-9393-6569"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]},{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]},{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}],"countries":["ES","IT","US"],"is_corresponding":false,"raw_author_name":"Roger Olivella","raw_affiliation_strings":["Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain, 2Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy, 3California Institute for Quantitative Biomedical Research (qb3) and Department of Bioengineering and Therapeutic Sciences, MC 2530, University of California San Francisco (UCSF) CA 94158\u20132330, USA and 4Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, 08010 Barcelona, Spain","Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain, 2Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy, 3California Institute for Quantitative Biomedical Research (qb3) and Department of Bioengineering and Therapeutic Sciences, MC 2530, University of California San Francisco (UCSF) CA 94158\u20132330, USA and 4Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, 08010 Barcelona, Spain","institution_ids":["https://openalex.org/I4210151238","https://openalex.org/I4210122345","https://openalex.org/I180670191","https://openalex.org/I9617848","https://openalex.org/I11932220","https://openalex.org/I30771326"]},{"raw_affiliation_string":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats, Barcelona, Spain","institution_ids":["https://openalex.org/I11932220"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015088787","display_name":"Patrick Aloy","orcid":"https://orcid.org/0000-0002-3557-0236"},"institutions":[{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]},{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]},{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]},{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["ES","IT","US"],"is_corresponding":false,"raw_author_name":"Patrick Aloy","raw_affiliation_strings":["Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain, 2Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy, 3California Institute for Quantitative Biomedical Research (qb3) and Department of Bioengineering and Therapeutic Sciences, MC 2530, University of California San Francisco (UCSF) CA 94158\u20132330, USA and 4Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, 08010 Barcelona, Spain","Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain, 2Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy, 3California Institute for Quantitative Biomedical Research (qb3) and Department of Bioengineering and Therapeutic Sciences, MC 2530, University of California San Francisco (UCSF) CA 94158\u20132330, USA and 4Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, 08010 Barcelona, Spain","institution_ids":["https://openalex.org/I4210151238","https://openalex.org/I4210122345","https://openalex.org/I180670191","https://openalex.org/I9617848","https://openalex.org/I11932220","https://openalex.org/I30771326"]},{"raw_affiliation_string":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats, Barcelona, Spain","institution_ids":["https://openalex.org/I11932220"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5013423377"],"corresponding_institution_ids":["https://openalex.org/I11932220"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":8.2358,"has_fulltext":true,"cited_by_count":326,"citation_normalized_percentile":{"value":0.98301495,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"42","issue":"D1","first_page":"D374","last_page":"D379"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9990000128746033,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9990000128746033,"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":0.9811999797821045,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9769999980926514,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"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/template","display_name":"Template","score":0.6403119564056396},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6331655383110046},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6108371019363403},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5914524793624878},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5884935855865479},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5819396376609802},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5356943607330322},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.5189540386199951},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.5100501179695129},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.45543819665908813},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.43325820565223694},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4093935191631317},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3808201253414154},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3496123254299164},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34949958324432373},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.323081374168396},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1647573709487915},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.160798579454422}],"concepts":[{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.6403119564056396},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6331655383110046},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6108371019363403},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5914524793624878},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5884935855865479},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5819396376609802},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5356943607330322},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5189540386199951},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.5100501179695129},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.45543819665908813},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.43325820565223694},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4093935191631317},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3808201253414154},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3496123254299164},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34949958324432373},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.323081374168396},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1647573709487915},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.160798579454422},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","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},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkt887","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt887","pdf_url":"https://academic.oup.com/nar/article-pdf/42/D1/D374/3670559/gkt887.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:24081580","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24081580","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:europepmc.org:2943138","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3965002","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.801.7456","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.801.7456","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/77/7b/gkt887.PMC3965002.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkt887","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt887","pdf_url":"https://academic.oup.com/nar/article-pdf/42/D1/D374/3670559/gkt887.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3027037052","display_name":null,"funder_award_id":"SyStemAge","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6868778225","display_name":null,"funder_award_id":"306240","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8051717526","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2031616673.pdf","grobid_xml":"https://content.openalex.org/works/W2031616673.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1566952502","https://openalex.org/W1965379872","https://openalex.org/W1969538102","https://openalex.org/W1975449945","https://openalex.org/W1975633255","https://openalex.org/W1985153601","https://openalex.org/W1988422871","https://openalex.org/W1994803330","https://openalex.org/W1998569806","https://openalex.org/W2010825547","https://openalex.org/W2049091299","https://openalex.org/W2083747978","https://openalex.org/W2083978969","https://openalex.org/W2085145974","https://openalex.org/W2085277871","https://openalex.org/W2085963663","https://openalex.org/W2101330776","https://openalex.org/W2101335101","https://openalex.org/W2107249189","https://openalex.org/W2108203465","https://openalex.org/W2109248504","https://openalex.org/W2122884883","https://openalex.org/W2126498993","https://openalex.org/W2128888818","https://openalex.org/W2130675570","https://openalex.org/W2135081201","https://openalex.org/W2135621733","https://openalex.org/W2140798893","https://openalex.org/W2141885858","https://openalex.org/W2143593035","https://openalex.org/W2143685757","https://openalex.org/W2148315081","https://openalex.org/W2152416668","https://openalex.org/W2155204211","https://openalex.org/W2160232999","https://openalex.org/W2168708922","https://openalex.org/W4256395558","https://openalex.org/W4320301318"],"related_works":["https://openalex.org/W2800059693","https://openalex.org/W2163614321","https://openalex.org/W37860747","https://openalex.org/W2066232588","https://openalex.org/W4377086792","https://openalex.org/W2010825547","https://openalex.org/W1574952448","https://openalex.org/W2352559055","https://openalex.org/W2026342583","https://openalex.org/W1843018858"],"abstract_inverted_index":{"The":[0,51],"database":[1],"of":[2,19,37,63,90,100,106],"3D":[3,26],"interacting":[4],"domains":[5],"(3did,":[6],"available":[7],"online":[8],"for":[9,22,48,58,102],"browsing":[10],"and":[11,32,61,72],"bulk":[12],"download":[13],"at":[14],"http://3did.irbbarcelona.org)":[15],"is":[16,28,96,111],"a":[17,24,56,86,97],"catalog":[18],"protein-protein":[20],"interactions":[21,39],"which":[23],"high-resolution":[25],"structure":[27],"known.":[29],"3did":[30,70,95,110],"collects":[31],"classifies":[33],"all":[34],"structural":[35,92,104],"templates":[36],"domain-domain":[38],"in":[40],"the":[41,59,103],"Protein":[42],"Data":[43],"Bank,":[44],"providing":[45],"molecular":[46],"details":[47],"such":[49],"interactions.":[50,66],"current":[52],"version":[53],"also":[54],"includes":[55],"pipeline":[57],"discovery":[60],"annotation":[62],"novel":[64],"domain-motif":[65],"For":[67],"every":[68,113],"interaction,":[69],"identifies":[71],"groups":[73],"different":[74],"binding":[75],"modes":[76],"by":[77],"clustering":[78],"similar":[79],"interfaces":[80],"into":[81],"'interaction":[82],"topologies'.":[83],"By":[84],"maintaining":[85],"constantly":[87],"updated":[88,112],"collection":[89],"domain-based":[91],"interaction":[93,108],"templates,":[94],"reference":[98],"source":[99],"information":[101],"characterization":[105],"protein":[107],"networks.":[109],"6":[114],"months.":[115]},"counts_by_year":[{"year":2026,"cited_by_count":12},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":25},{"year":2022,"cited_by_count":26},{"year":2021,"cited_by_count":39},{"year":2020,"cited_by_count":26},{"year":2019,"cited_by_count":32},{"year":2018,"cited_by_count":35},{"year":2017,"cited_by_count":30},{"year":2016,"cited_by_count":20},{"year":2015,"cited_by_count":17},{"year":2014,"cited_by_count":17},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}
