{"id":"https://openalex.org/W2137635996","doi":"https://doi.org/10.1093/bioinformatics/btp238","title":"ModLink+: improving fold recognition by using protein\u2013protein interactions","display_name":"ModLink+: improving fold recognition by using protein\u2013protein interactions","publication_year":2009,"publication_date":"2009-04-08","ids":{"openalex":"https://openalex.org/W2137635996","doi":"https://doi.org/10.1093/bioinformatics/btp238","mag":"2137635996","pmid":"https://pubmed.ncbi.nlm.nih.gov/19357100"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp238","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp238","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/1506/48992258/bioinformatics_25_12_1506.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/25/12/1506/48992258/bioinformatics_25_12_1506.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065435409","display_name":"Oriol Forn\u00e9s","orcid":"https://orcid.org/0000-0002-5969-3054"},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]},{"id":"https://openalex.org/I4210165109","display_name":"Centro de Investigacion Principe Felipe","ror":"https://ror.org/05xr2yq54","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210165109"]}],"countries":["ES","US"],"is_corresponding":false,"raw_author_name":"Oriol Fornes","raw_affiliation_strings":["1 Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Parc de Recerca Biom\u00e8dica de Barcelona (PRBB), Barcelona, Catalonia, 2Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain, 3Department of Bioengineering and Therapeutic Sciences, 4Department of Pharmaceutical Chemistry and 5California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Parc de Recerca Biom\u00e8dica de Barcelona (PRBB), Barcelona, Catalonia, 2Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain, 3Department of Bioengineering and Therapeutic Sciences, 4Department of Pharmaceutical Chemistry and 5California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I170486558","https://openalex.org/I2801864671","https://openalex.org/I4210165109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005359314","display_name":"Ram\u00f3n Arag\u00fc\u00e9s","orcid":null},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]},{"id":"https://openalex.org/I4210165109","display_name":"Centro de Investigacion Principe Felipe","ror":"https://ror.org/05xr2yq54","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210165109"]}],"countries":["ES","US"],"is_corresponding":false,"raw_author_name":"Ramon Aragues","raw_affiliation_strings":["1 Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Parc de Recerca Biom\u00e8dica de Barcelona (PRBB), Barcelona, Catalonia, 2Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain, 3Department of Bioengineering and Therapeutic Sciences, 4Department of Pharmaceutical Chemistry and 5California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Parc de Recerca Biom\u00e8dica de Barcelona (PRBB), Barcelona, Catalonia, 2Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain, 3Department of Bioengineering and Therapeutic Sciences, 4Department of Pharmaceutical Chemistry and 5California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I170486558","https://openalex.org/I2801864671","https://openalex.org/I4210165109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044431149","display_name":"Jordi Espadaler","orcid":"https://orcid.org/0000-0002-0128-8363"},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]},{"id":"https://openalex.org/I4210165109","display_name":"Centro de Investigacion Principe Felipe","ror":"https://ror.org/05xr2yq54","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210165109"]}],"countries":["ES","US"],"is_corresponding":false,"raw_author_name":"Jordi Espadaler","raw_affiliation_strings":["1 Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Parc de Recerca Biom\u00e8dica de Barcelona (PRBB), Barcelona, Catalonia, 2Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain, 3Department of Bioengineering and Therapeutic Sciences, 4Department of Pharmaceutical Chemistry and 5California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Parc de Recerca Biom\u00e8dica de Barcelona (PRBB), Barcelona, Catalonia, 2Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain, 3Department of Bioengineering and Therapeutic Sciences, 4Department of Pharmaceutical Chemistry and 5California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I170486558","https://openalex.org/I2801864671","https://openalex.org/I4210165109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082758634","display_name":"Marc A. Mart\u0131\u0301-Renom","orcid":"https://orcid.org/0000-0002-0151-4279"},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]},{"id":"https://openalex.org/I4210165109","display_name":"Centro de Investigacion Principe Felipe","ror":"https://ror.org/05xr2yq54","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210165109"]}],"countries":["ES","US"],"is_corresponding":false,"raw_author_name":"Marc A. Marti-Renom","raw_affiliation_strings":["1 Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Parc de Recerca Biom\u00e8dica de Barcelona (PRBB), Barcelona, Catalonia, 2Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain, 3Department of Bioengineering and Therapeutic Sciences, 4Department of Pharmaceutical Chemistry and 5California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Parc de Recerca Biom\u00e8dica de Barcelona (PRBB), Barcelona, Catalonia, 2Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain, 3Department of Bioengineering and Therapeutic Sciences, 4Department of Pharmaceutical Chemistry and 5California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I170486558","https://openalex.org/I2801864671","https://openalex.org/I4210165109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028845140","display_name":"Andrej \u0160ali","orcid":"https://orcid.org/0000-0003-0435-6197"},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]},{"id":"https://openalex.org/I4210165109","display_name":"Centro de Investigacion Principe Felipe","ror":"https://ror.org/05xr2yq54","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210165109"]}],"countries":["ES","US"],"is_corresponding":false,"raw_author_name":"Andrej Sali","raw_affiliation_strings":["1 Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Parc de Recerca Biom\u00e8dica de Barcelona (PRBB), Barcelona, Catalonia, 2Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain, 3Department of Bioengineering and Therapeutic Sciences, 4Department of Pharmaceutical Chemistry and 5California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Parc de Recerca Biom\u00e8dica de Barcelona (PRBB), Barcelona, Catalonia, 2Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain, 3Department of Bioengineering and Therapeutic Sciences, 4Department of Pharmaceutical Chemistry and 5California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I170486558","https://openalex.org/I2801864671","https://openalex.org/I4210165109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111840557","display_name":"Baldo Oliva","orcid":null},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]},{"id":"https://openalex.org/I4210165109","display_name":"Centro de Investigacion Principe Felipe","ror":"https://ror.org/05xr2yq54","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210165109"]}],"countries":["ES","US"],"is_corresponding":true,"raw_author_name":"Baldo Oliva","raw_affiliation_strings":["1 Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Parc de Recerca Biom\u00e8dica de Barcelona (PRBB), Barcelona, Catalonia, 2Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain, 3Department of Bioengineering and Therapeutic Sciences, 4Department of Pharmaceutical Chemistry and 5California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Parc de Recerca Biom\u00e8dica de Barcelona (PRBB), Barcelona, Catalonia, 2Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain, 3Department of Bioengineering and Therapeutic Sciences, 4Department of Pharmaceutical Chemistry and 5California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I170486558","https://openalex.org/I2801864671","https://openalex.org/I4210165109"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5111840557"],"corresponding_institution_ids":["https://openalex.org/I103922791","https://openalex.org/I170486558","https://openalex.org/I2801864671","https://openalex.org/I4210165109"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8819,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.72986334,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"25","issue":"12","first_page":"1506","last_page":"1512"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.6991999745368958,"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":0.6991999745368958,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.07819999754428864,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0737999975681305,"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/fold","display_name":"Fold (higher-order function)","score":0.6851322650909424},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5962983965873718},{"id":"https://openalex.org/keywords/test-set","display_name":"Test set","score":0.5392829775810242},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.5350139737129211},{"id":"https://openalex.org/keywords/cutoff","display_name":"Cutoff","score":0.4603016972541809},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.44135579466819763},{"id":"https://openalex.org/keywords/value","display_name":"Value (mathematics)","score":0.43953847885131836},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4258577525615692},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4172077178955078},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39395982027053833},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3272375464439392},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3233581781387329},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2921369969844818},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2913079857826233},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22955986857414246},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.21025103330612183},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.17993533611297607},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.11723896861076355}],"concepts":[{"id":"https://openalex.org/C53942344","wikidata":"https://www.wikidata.org/wiki/Q951651","display_name":"Fold (higher-order function)","level":2,"score":0.6851322650909424},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5962983965873718},{"id":"https://openalex.org/C169903167","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Test set","level":2,"score":0.5392829775810242},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.5350139737129211},{"id":"https://openalex.org/C2778217198","wikidata":"https://www.wikidata.org/wiki/Q556977","display_name":"Cutoff","level":2,"score":0.4603016972541809},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.44135579466819763},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.43953847885131836},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4258577525615692},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4172077178955078},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39395982027053833},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3272375464439392},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3233581781387329},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2921369969844818},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2913079857826233},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22955986857414246},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.21025103330612183},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.17993533611297607},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.11723896861076355},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","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":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":false},{"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp238","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp238","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/1506/48992258/bioinformatics_25_12_1506.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":"pmh:oai:pubmedcentral.nih.gov:2687990","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2687990","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmid:19357100","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19357100","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":{"id":"doi:10.1093/bioinformatics/btp238","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp238","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/1506/48992258/bioinformatics_25_12_1506.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":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G2451876725","display_name":null,"funder_award_id":"R01 GM054762","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3130799967","display_name":null,"funder_award_id":"U54 RR022220","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G3594440153","display_name":"Protein Modeling by Satisfaction of Spatial Restraints","funder_award_id":"5r01gm054762-14","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4823872311","display_name":"New Tools for Exploring the Dynamic Interactome (Renewal)","funder_award_id":"2u54rr022220-06","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G565063786","display_name":null,"funder_award_id":"R01 GM54762","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5849660352","display_name":null,"funder_award_id":"U54 GM074945","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7466557775","display_name":"NYSGXRC:A Large Scale Center for the PSI","funder_award_id":"5u54gm074945-06","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320316505","display_name":"NetApp","ror":"https://ror.org/05c4cm338"},{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320323868","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2137635996.pdf","grobid_xml":"https://content.openalex.org/works/W2137635996.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1534270226","https://openalex.org/W1977538576","https://openalex.org/W1980800453","https://openalex.org/W1988422871","https://openalex.org/W1999548303","https://openalex.org/W2001457899","https://openalex.org/W2010485601","https://openalex.org/W2014777266","https://openalex.org/W2014926036","https://openalex.org/W2020644553","https://openalex.org/W2021639324","https://openalex.org/W2037442572","https://openalex.org/W2039465881","https://openalex.org/W2041938888","https://openalex.org/W2051969447","https://openalex.org/W2072133388","https://openalex.org/W2084466582","https://openalex.org/W2085145974","https://openalex.org/W2087574732","https://openalex.org/W2094090446","https://openalex.org/W2095627884","https://openalex.org/W2097698606","https://openalex.org/W2099667027","https://openalex.org/W2100063856","https://openalex.org/W2101330776","https://openalex.org/W2103729016","https://openalex.org/W2106868489","https://openalex.org/W2118836759","https://openalex.org/W2128653811","https://openalex.org/W2129996459","https://openalex.org/W2130479394","https://openalex.org/W2130675570","https://openalex.org/W2130687290","https://openalex.org/W2132122858","https://openalex.org/W2138351249","https://openalex.org/W2140776132","https://openalex.org/W2141885858","https://openalex.org/W2143011057","https://openalex.org/W2145268834","https://openalex.org/W2146134187","https://openalex.org/W2147736120","https://openalex.org/W2151831732","https://openalex.org/W2152281406","https://openalex.org/W2152444476","https://openalex.org/W2152653671","https://openalex.org/W2153187042","https://openalex.org/W2158714788","https://openalex.org/W2161062388","https://openalex.org/W2164391585","https://openalex.org/W2166043581","https://openalex.org/W2166468869","https://openalex.org/W2169356867","https://openalex.org/W2169408159","https://openalex.org/W2916288174","https://openalex.org/W2917431650","https://openalex.org/W4210323379","https://openalex.org/W4285719527","https://openalex.org/W6681134107"],"related_works":["https://openalex.org/W1181095405","https://openalex.org/W3092388660","https://openalex.org/W1778838665","https://openalex.org/W3014426369","https://openalex.org/W4240318783","https://openalex.org/W3175879137","https://openalex.org/W2328322229","https://openalex.org/W2311285072","https://openalex.org/W1573293794","https://openalex.org/W2119262383"],"abstract_inverted_index":{"MOTIVATION:":[0],"Several":[1],"strategies":[2],"have":[3],"been":[4,99],"developed":[5],"to":[6,25,63,88,155,171,189],"predict":[7],"the":[8,22,35,42,58,77,109,122,132,159,174,177,196,237,247],"fold":[9,45,66,91,141,170,194,204],"of":[10,16,28,37,44,54,61,76,124,134,162,173],"a":[11,65,169,203,224,230],"target":[12,23],"protein":[13],"sequence,":[14],"most":[15],"which":[17,64],"are":[18,257],"based":[19],"on":[20,101,140],"aligning":[21],"sequence":[24,50],"other":[26,89],"sequences":[27],"known":[29,118],"structure.":[30],"Previously,":[31],"we":[32,71],"demonstrated":[33],"that":[34,79,227],"consideration":[36],"protein-protein":[38],"interactions":[39],"significantly":[40],"increases":[41,143],"accuracy":[43],"assignment":[46,92,142],"compared":[47],"with":[48,104,192,200],"PSI-BLAST":[49,201,211],"comparisons.":[51],"A":[52],"drawback":[53],"our":[55,86,181],"method":[56,78,87,183,235],"was":[57],"low":[59],"number":[60],"proteins":[62,103,175,191],"could":[67,184],"be":[68],"assigned.":[69],"Here,":[70],"present":[72],"an":[73],"improved":[74],"version":[75],"addresses":[80],"this":[81,129,165],"limitation.":[82],"We":[83],"also":[84],"compare":[85],"state-of-the-art":[90],"methodologies.":[93],"RESULTS:":[94],"Our":[95],"approach":[96],"(ModLink+)":[97],"has":[98],"tested":[100],"3716":[102],"domain":[105],"folds":[106],"classified":[107],"in":[108,121,176,195,207,236,246],"Structural":[110],"Classification":[111],"Of":[112],"Proteins":[113,126],"(SCOP)":[114],"as":[115,117],"well":[116],"interacting":[119],"partners":[120],"Database":[123],"Interacting":[125],"(DIP).":[127],"For":[128],"test":[130,178,238],"set,":[131,179],"ratio":[133],"success":[135],"[positive":[136],"predictive":[137],"value":[138],"(PPV)]":[139],"from":[144],"75%":[145],"for":[146,149,153,157,205,233],"PSI-BLAST,":[147],"83%":[148],"HHSearch":[150,217],"and":[151,219],"81%":[152],"PRC":[154,220],">90%":[156],"ModLink+at":[158],"e-value":[160,226],"cutoff":[161],"10(-3).":[163],"Under":[164],"e-value,":[166],"ModLink+can":[167],"assign":[168],"30-45%":[172],"while":[180,210],"previous":[182],"cover":[185],"<25%.":[186],"When":[187],"applied":[188],"6384":[190],"unknown":[193],"yeast":[197],"proteome,":[198],"ModLink+combined":[199],"assigns":[202],"domains":[206],"3738":[208],"proteins,":[209,216,222],"alone":[212],"covers":[213],"only":[214],"2122":[215],"2969":[218],"2826":[221],"using":[223],"threshold":[225],"would":[228],"represent":[229],"PPV":[231],">82%":[232],"each":[234],"set.":[239],"AVAILABILITY:":[240],"The":[241],"ModLink+server":[242],"is":[243],"freely":[244],"accessible":[245],"World":[248],"Wide":[249],"Web":[250],"at":[251,259],"http://sbi.imim.es/modlink/.":[252],"SUPPLEMENTARY":[253],"INFORMATION:":[254],"Supplementary":[255],"data":[256],"available":[258],"Bioinformatics":[260],"online.":[261]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
