{"id":"https://openalex.org/W2108125432","doi":"https://doi.org/10.1093/bioinformatics/btq657","title":"A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain\u2013peptide interaction from primary sequence","display_name":"A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain\u2013peptide interaction from primary sequence","publication_year":2010,"publication_date":"2010-12-02","ids":{"openalex":"https://openalex.org/W2108125432","doi":"https://doi.org/10.1093/bioinformatics/btq657","mag":"2108125432","pmid":"https://pubmed.ncbi.nlm.nih.gov/21127034"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq657","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq657","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/3/383/48864086/bioinformatics_27_3_383.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/3/383/48864086/bioinformatics_27_3_383.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001145592","display_name":"Xiaojian Shao","orcid":"https://orcid.org/0000-0002-3044-621X"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"Xiaojian Shao","raw_affiliation_strings":["1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada","institution_ids":["https://openalex.org/I125749732","https://openalex.org/I185261750","https://openalex.org/I52158045"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051693291","display_name":"Chris Soon Heng Tan","orcid":"https://orcid.org/0000-0002-8172-5235"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"Chris S. H. Tan","raw_affiliation_strings":["1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada","institution_ids":["https://openalex.org/I125749732","https://openalex.org/I185261750","https://openalex.org/I52158045"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025074515","display_name":"Courtney Voss","orcid":"https://orcid.org/0000-0002-9460-9866"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"Courtney Voss","raw_affiliation_strings":["1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada","institution_ids":["https://openalex.org/I125749732","https://openalex.org/I185261750","https://openalex.org/I52158045"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018410197","display_name":"Shawn S.\u2010C. Li","orcid":"https://orcid.org/0000-0003-3610-9035"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"Shawn S. C. Li","raw_affiliation_strings":["1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada","institution_ids":["https://openalex.org/I125749732","https://openalex.org/I185261750","https://openalex.org/I52158045"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113564486","display_name":"Nai-Yang Deng","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CA","CN"],"is_corresponding":true,"raw_author_name":"Naiyang Deng","raw_affiliation_strings":["1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada","institution_ids":["https://openalex.org/I125749732","https://openalex.org/I185261750","https://openalex.org/I52158045"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010789029","display_name":"Gary D. Bader","orcid":"https://orcid.org/0000-0003-0185-8861"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CA","CN"],"is_corresponding":true,"raw_author_name":"Gary D. Bader","raw_affiliation_strings":["1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada","institution_ids":["https://openalex.org/I125749732","https://openalex.org/I185261750","https://openalex.org/I52158045"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5010789029","https://openalex.org/A5113564486"],"corresponding_institution_ids":["https://openalex.org/I125749732","https://openalex.org/I185261750","https://openalex.org/I52158045"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.7458,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.83058127,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"27","issue":"3","first_page":"383","last_page":"390"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12065","display_name":"Hippo pathway signaling and YAP/TAZ","score":0.3619999885559082,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T12065","display_name":"Hippo pathway signaling and YAP/TAZ","score":0.3619999885559082,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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":0.16760000586509705,"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":0.09049999713897705,"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/pdz-domain","display_name":"PDZ domain","score":0.9734714031219482},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6188277006149292},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5958455801010132},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5873011350631714},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5369176268577576},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.4895857274532318},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.48611927032470703},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.48318949341773987},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4479205906391144},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.42533156275749207},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39905646443367004},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35407811403274536},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3346378803253174},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2866842448711395},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17568925023078918},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.15025591850280762},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08818954229354858}],"concepts":[{"id":"https://openalex.org/C154428179","wikidata":"https://www.wikidata.org/wiki/Q24721050","display_name":"PDZ domain","level":2,"score":0.9734714031219482},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6188277006149292},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5958455801010132},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5873011350631714},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5369176268577576},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.4895857274532318},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.48611927032470703},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.48318949341773987},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4479205906391144},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.42533156275749207},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39905646443367004},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35407811403274536},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3346378803253174},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2866842448711395},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17568925023078918},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.15025591850280762},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08818954229354858},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","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":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054731","descriptor_name":"PDZ Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054731","descriptor_name":"PDZ Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054731","descriptor_name":"PDZ Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btq657","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq657","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/3/383/48864086/bioinformatics_27_3_383.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21127034","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21127034","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:ir.lib.uwo.ca:biochempub-1145","is_oa":false,"landing_page_url":"https://ir.lib.uwo.ca/biochempub/143","pdf_url":null,"source":{"id":"https://openalex.org/S4306400648","display_name":"Scholarship@Western (Western University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I125749732","host_organization_name":"Western University","host_organization_lineage":["https://openalex.org/I125749732"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Biochemistry Publications","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3031032","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3031032","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq657","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq657","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/3/383/48864086/bioinformatics_27_3_383.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.4399999976158142,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G3528054200","display_name":null,"funder_award_id":"MOP-84324","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1493799579","https://openalex.org/W1584120419","https://openalex.org/W1852635481","https://openalex.org/W1964357740","https://openalex.org/W1967195968","https://openalex.org/W1968442411","https://openalex.org/W1973858755","https://openalex.org/W1975633255","https://openalex.org/W1985446591","https://openalex.org/W1990800680","https://openalex.org/W1994996237","https://openalex.org/W2021620380","https://openalex.org/W2024962796","https://openalex.org/W2037656549","https://openalex.org/W2054711926","https://openalex.org/W2063092201","https://openalex.org/W2066059461","https://openalex.org/W2074570440","https://openalex.org/W2077550665","https://openalex.org/W2092006899","https://openalex.org/W2099982459","https://openalex.org/W2100549317","https://openalex.org/W2111066113","https://openalex.org/W2118471957","https://openalex.org/W2119279196","https://openalex.org/W2125644345","https://openalex.org/W2127455622","https://openalex.org/W2132056336","https://openalex.org/W2133070552","https://openalex.org/W2137104501","https://openalex.org/W2140933450","https://openalex.org/W2140996283","https://openalex.org/W2142873050","https://openalex.org/W2145080853","https://openalex.org/W2147202073","https://openalex.org/W2149769193","https://openalex.org/W2151457629","https://openalex.org/W2152800101","https://openalex.org/W2152991541","https://openalex.org/W2153635508","https://openalex.org/W2154392018","https://openalex.org/W2164076798","https://openalex.org/W2171096262","https://openalex.org/W3120421331","https://openalex.org/W4249920046","https://openalex.org/W6634814127"],"related_works":["https://openalex.org/W2913537206","https://openalex.org/W2014235532","https://openalex.org/W1981740764","https://openalex.org/W2275510245","https://openalex.org/W2207139036","https://openalex.org/W2162151490","https://openalex.org/W2066353226","https://openalex.org/W2115050780","https://openalex.org/W2132186283","https://openalex.org/W1970431511"],"abstract_inverted_index":{"MOTIVATION:":[0],"Predicting":[1],"protein":[2,37],"interactions":[3,29,74,115],"involving":[4,116],"peptide":[5,80,86],"recognition":[6,81],"domains":[7,70,120],"is":[8,20,97,160],"essential":[9],"for":[10,67,175,189],"understanding":[11],"the":[12,24,110],"many":[13],"important":[14,21,162],"biological":[15],"processes":[16],"they":[17],"mediate.":[18],"It":[19],"to":[22,30,71,99,108],"consider":[23,41],"binding":[25,112],"strength":[26,113],"of":[27,114],"these":[28],"help":[31],"us":[32],"construct":[33],"more":[34],"biologically":[35],"relevant":[36],"interaction":[38,64,106,152,173],"networks":[39],"that":[40,56,95,146,157,168],"cellular":[42],"context":[43],"and":[44,61,84,104,135,193],"competition":[45],"between":[46,75],"potential":[47],"binders.":[48],"RESULTS:":[49],"We":[50],"developed":[51],"a":[52,78],"novel":[53],"regression":[54],"framework":[55],"considers":[57],"both":[58],"positive":[59],"(quantitative)":[60],"negative":[62,105,148],"(qualitative)":[63],"data":[65,107,149,174,195],"available":[66,199],"mouse":[68],"PDZ":[69,76,119,140,177],"quantitatively":[72],"predict":[73],"domains,":[77],"large":[79],"domain":[82,178],"family,":[83],"their":[85,124],"ligands":[87],"using":[88,130],"primary":[89,125],"sequence":[90,158],"information.":[91],"First,":[92],"we":[93,144,155],"show":[94,156],"it":[96],"possible":[98],"learn":[100],"from":[101],"existing":[102],"quantitative":[103,151,172],"infer":[109],"relative":[111],"previously":[117,138],"unseen":[118,139],"and/or":[121],"peptides":[122],"given":[123],"sequence.":[126],"Performance":[127],"was":[128],"measured":[129],"cross-validated":[131],"hold":[132],"out":[133],"testing":[134,136],"with":[137],"domain-peptide":[141],"interactions.":[142],"Second,":[143],"find":[145],"incorporating":[147],"improves":[150],"prediction.":[153,182],"Third,":[154],"similarity":[159],"an":[161],"prediction":[163],"performance":[164],"determinant,":[165],"which":[166],"suggests":[167],"experimentally":[169],"collecting":[170],"additional":[171],"underrepresented":[176],"subfamilies":[179],"will":[180],"improve":[181],"AVAILABILITY":[183],"AND":[184],"IMPLEMENTATION:":[185],"The":[186],"Matlab":[187],"code":[188],"our":[190],"SemiSVR":[191],"predictor":[192],"all":[194],"used":[196],"here":[197],"are":[198],"at":[200],"http://baderlab.org/Data/PDZAffinity.":[201]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":5}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
