{"id":"https://openalex.org/W267236089","doi":"https://doi.org/10.1371/journal.pcbi.1004248","title":"Predicting Peptide-Mediated Interactions on a Genome-Wide Scale","display_name":"Predicting Peptide-Mediated Interactions on a Genome-Wide Scale","publication_year":2015,"publication_date":"2015-05-04","ids":{"openalex":"https://openalex.org/W267236089","doi":"https://doi.org/10.1371/journal.pcbi.1004248","mag":"267236089","pmid":"https://pubmed.ncbi.nlm.nih.gov/25938916"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004248","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004248","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004248&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004248&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027612916","display_name":"T. Scott Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. Scott Chen","raw_affiliation_strings":["Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America; Department of Systems Biology, Columbia University, New York, New York, United States of America; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America; Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America","Department of Systems Biology, Columbia University, New York, New York, United States of America","Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America; Department of Systems Biology, Columbia University, New York, New York, United States of America; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America; Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","institution_ids":[]},{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Systems Biology, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020269639","display_name":"Donald Petrey","orcid":null},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]},{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Donald Petrey","raw_affiliation_strings":["Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America; Department of Systems Biology, Columbia University, New York, New York, United States of America; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America; Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America","Department of Systems Biology, Columbia University, New York, New York, United States of America","Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America; Department of Systems Biology, Columbia University, New York, New York, United States of America; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America; Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","institution_ids":[]},{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Systems Biology, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005566175","display_name":"Jos\u00e9 Ignacio Garz\u00f3n","orcid":null},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jose Ignacio Garzon","raw_affiliation_strings":["Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America; Department of Systems Biology, Columbia University, New York, New York, United States of America; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America; Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America","Department of Systems Biology, Columbia University, New York, New York, United States of America","Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America","Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America; Department of Systems Biology, Columbia University, New York, New York, United States of America; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America; Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","institution_ids":[]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Systems Biology, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I78577930"]},{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036654109","display_name":"Barry Honig","orcid":"https://orcid.org/0000-0002-1835-1031"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]},{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Barry Honig","raw_affiliation_strings":["Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America; Department of Systems Biology, Columbia University, New York, New York, United States of America; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America; Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America","Department of Systems Biology, Columbia University, New York, New York, United States of America","Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America","Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America; Department of Systems Biology, Columbia University, New York, New York, United States of America; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America; Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","institution_ids":[]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Systems Biology, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I78577930"]},{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5036654109"],"corresponding_institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I78577930"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.3553,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.79722363,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"11","issue":"5","first_page":"e1004248","last_page":"e1004248"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9973000288009644,"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":0.9973000288009644,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.994700014591217,"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":0.9926000237464905,"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/interactome","display_name":"Interactome","score":0.7796793580055237},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6123818755149841},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5461819767951965},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5255861878395081},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.5164635181427002},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.45619824528694153},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.44870275259017944},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3950587511062622},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38910552859306335},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3779356777667999},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.36610472202301025},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34275972843170166},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29442256689071655},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17413648962974548},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09922441840171814},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08309832215309143}],"concepts":[{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.7796793580055237},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6123818755149841},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5461819767951965},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5255861878395081},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5164635181427002},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.45619824528694153},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.44870275259017944},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3950587511062622},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38910552859306335},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3779356777667999},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.36610472202301025},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34275972843170166},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29442256689071655},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17413648962974548},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09922441840171814},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08309832215309143}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","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":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1004248","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004248","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004248&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:25938916","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25938916","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:894ded1395b44302ae8197901d301530","is_oa":true,"landing_page_url":"https://doaj.org/article/894ded1395b44302ae8197901d301530","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 11, Iss 5, p e1004248 (2015)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/1403133","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Predicting_Peptide_Mediated_Interactions_on_a_Genome_Wide_Scale_/1403133","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:4418708","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4418708","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004248","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004248","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004248&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4284351861","display_name":null,"funder_award_id":"GM030518","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W267236089.pdf","grobid_xml":"https://content.openalex.org/works/W267236089.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1965379872","https://openalex.org/W1975622992","https://openalex.org/W1975633255","https://openalex.org/W1976526581","https://openalex.org/W1986751941","https://openalex.org/W1992983658","https://openalex.org/W1993279060","https://openalex.org/W1994891218","https://openalex.org/W2021620380","https://openalex.org/W2023272942","https://openalex.org/W2029574260","https://openalex.org/W2037442572","https://openalex.org/W2039473152","https://openalex.org/W2049349724","https://openalex.org/W2054954101","https://openalex.org/W2056097559","https://openalex.org/W2056264942","https://openalex.org/W2063092201","https://openalex.org/W2065921821","https://openalex.org/W2068590125","https://openalex.org/W2078336808","https://openalex.org/W2083747978","https://openalex.org/W2094131214","https://openalex.org/W2101763464","https://openalex.org/W2105924489","https://openalex.org/W2106315897","https://openalex.org/W2107424557","https://openalex.org/W2113654464","https://openalex.org/W2114306742","https://openalex.org/W2121507105","https://openalex.org/W2122863289","https://openalex.org/W2124463526","https://openalex.org/W2131736388","https://openalex.org/W2132926880","https://openalex.org/W2135621733","https://openalex.org/W2137104501","https://openalex.org/W2137239190","https://openalex.org/W2140996283","https://openalex.org/W2141885858","https://openalex.org/W2142883880","https://openalex.org/W2144145301","https://openalex.org/W2145080853","https://openalex.org/W2147610376","https://openalex.org/W2149310258","https://openalex.org/W2152336513","https://openalex.org/W2153018384","https://openalex.org/W2155320925","https://openalex.org/W2155723007","https://openalex.org/W2156407548","https://openalex.org/W2163485494","https://openalex.org/W2165958610","https://openalex.org/W2330547698","https://openalex.org/W2605068739","https://openalex.org/W4210623056","https://openalex.org/W4230842383"],"related_works":["https://openalex.org/W2152546257","https://openalex.org/W2018720220","https://openalex.org/W1500663296","https://openalex.org/W4252442860","https://openalex.org/W3159731292","https://openalex.org/W2178844921","https://openalex.org/W2162117109","https://openalex.org/W2392586760","https://openalex.org/W4319230148","https://openalex.org/W2157795344"],"abstract_inverted_index":{"We":[0,17,44],"describe":[1],"a":[2,51,86],"method":[3,90],"to":[4,69,75,97],"predict":[5],"protein-protein":[6],"interactions":[7,98,109],"(PPIs)":[8],"formed":[9,99],"between":[10,100],"structured":[11,102],"domains":[12],"and":[13,38,61,74],"short":[14],"peptide":[15],"motifs.":[16],"take":[18],"an":[19,59],"integrative":[20],"approach":[21,81],"based":[22],"on":[23],"consensus":[24],"patterns":[25],"of":[26,32,41,48,58,72,116],"known":[27],"motifs":[28],"in":[29],"databases,":[30],"structures":[31],"domain-motif":[33,107],"complexes":[34],"from":[35],"the":[36,56,117],"PDB":[37],"various":[39],"sources":[40,71],"non-structural":[42],"evidence.":[43],"combine":[45],"this":[46],"set":[47],"clues":[49],"using":[50],"Bayesian":[52,80],"classifier":[53],"that":[54],"reports":[55],"likelihood":[57],"interaction":[60],"obtain":[62],"significantly":[63],"improved":[64],"prediction":[65,89],"performance":[66],"when":[67],"compared":[68],"individual":[70],"evidence":[73],"previously":[76],"reported":[77],"algorithms.":[78],"Our":[79],"was":[82],"integrated":[83],"into":[84],"PrePPI,":[85],"structure-based":[87],"PPI":[88],"that,":[91],"so":[92],"far,":[93],"has":[94],"been":[95],"limited":[96],"two":[101],"domains.":[103],"Around":[104],"80,000":[105],"new":[106],"mediated":[108],"were":[110],"predicted,":[111],"thus":[112],"enhancing":[113],"PrePPI's":[114],"coverage":[115],"human":[118],"protein":[119],"interactome.":[120]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}