{"id":"https://openalex.org/W1963911475","doi":"https://doi.org/10.1186/1471-2105-11-357","title":"Interaction prediction and classification of PDZ domains","display_name":"Interaction prediction and classification of PDZ domains","publication_year":2010,"publication_date":"2010-06-30","ids":{"openalex":"https://openalex.org/W1963911475","doi":"https://doi.org/10.1186/1471-2105-11-357","mag":"1963911475","pmid":"https://pubmed.ncbi.nlm.nih.gov/20591147"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-357","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-357","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-357","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-357","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084751225","display_name":"Sibel Kalyoncu","orcid":"https://orcid.org/0000-0003-2264-0757"},"institutions":[{"id":"https://openalex.org/I1351752","display_name":"Ko\u00e7 University","ror":"https://ror.org/00jzwgz36","country_code":"TR","type":"education","lineage":["https://openalex.org/I1351752"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Sibel Kalyoncu","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Rumelifeneri Yolu 34450 Sariyer, Istanbul, Turkey","Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Sariyer, Turkey"],"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Rumelifeneri Yolu 34450 Sariyer, Istanbul, Turkey","institution_ids":["https://openalex.org/I1351752"]},{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Sariyer, Turkey","institution_ids":["https://openalex.org/I1351752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057115991","display_name":"\u00d6zlem Keskin","orcid":"https://orcid.org/0000-0002-4202-4049"},"institutions":[{"id":"https://openalex.org/I1351752","display_name":"Ko\u00e7 University","ror":"https://ror.org/00jzwgz36","country_code":"TR","type":"education","lineage":["https://openalex.org/I1351752"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Ozlem Keskin","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Rumelifeneri Yolu, 34450, Sariyer, Istanbul, Turkey","Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Sariyer, Turkey"],"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Rumelifeneri Yolu, 34450, Sariyer, Istanbul, Turkey","institution_ids":["https://openalex.org/I1351752"]},{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Sariyer, Turkey","institution_ids":["https://openalex.org/I1351752"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036278069","display_name":"Attila G\u00fcrsoy","orcid":"https://orcid.org/0000-0002-2297-2113"},"institutions":[{"id":"https://openalex.org/I1351752","display_name":"Ko\u00e7 University","ror":"https://ror.org/00jzwgz36","country_code":"TR","type":"education","lineage":["https://openalex.org/I1351752"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Attila Gursoy","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Rumelifeneri Yolu, 34450, Sariyer, Istanbul, Turkey","Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Sariyer, Turkey"],"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Rumelifeneri Yolu, 34450, Sariyer, Istanbul, Turkey","institution_ids":["https://openalex.org/I1351752"]},{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Sariyer, Turkey","institution_ids":["https://openalex.org/I1351752"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5084751225"],"corresponding_institution_ids":["https://openalex.org/I1351752"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":6.206,"has_fulltext":true,"cited_by_count":48,"citation_normalized_percentile":{"value":0.96577154,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"11","issue":"1","first_page":"357","last_page":"357"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9753999710083008,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9753999710083008,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9692999720573425,"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/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.9563000202178955,"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":0.9961060881614685},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5842723250389099},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4639323353767395},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.46273383498191833},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.43324604630470276},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3939668536186218},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2687172293663025},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12137702107429504}],"concepts":[{"id":"https://openalex.org/C154428179","wikidata":"https://www.wikidata.org/wiki/Q24721050","display_name":"PDZ domain","level":2,"score":0.9961060881614685},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5842723250389099},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4639323353767395},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.46273383498191833},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.43324604630470276},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3939668536186218},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2687172293663025},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12137702107429504}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","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":"D000818","descriptor_name":"Animals","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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","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":5,"locations":[{"id":"doi:10.1186/1471-2105-11-357","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-357","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-357","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20591147","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20591147","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:cdm21054.contentdm.oclc.org:IR/478","is_oa":false,"landing_page_url":"http://doi.org/10.1186/1471-2105-11-357","pdf_url":null,"source":{"id":"https://openalex.org/S4306401341","display_name":"Digital Collections portal (Ko\u00e7 University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1351752","host_organization_name":"Ko\u00e7 University","host_organization_lineage":["https://openalex.org/I1351752"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC bioinformatics","raw_type":"Journal article"},{"id":"pmh:oai:doaj.org/article:46065c00233e4e3f907a0835cbc84ace","is_oa":true,"landing_page_url":"https://doaj.org/article/46065c00233e4e3f907a0835cbc84ace","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss 1, p 357 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2909223","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2909223","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-357","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-357","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-357","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1963911475.pdf","grobid_xml":"https://content.openalex.org/works/W1963911475.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W110089190","https://openalex.org/W1502050276","https://openalex.org/W1504694836","https://openalex.org/W1526353609","https://openalex.org/W1570448133","https://openalex.org/W1817561967","https://openalex.org/W1974706357","https://openalex.org/W1976526581","https://openalex.org/W1979715740","https://openalex.org/W1982267716","https://openalex.org/W1985446591","https://openalex.org/W1987704449","https://openalex.org/W1988594478","https://openalex.org/W1990800680","https://openalex.org/W1996320892","https://openalex.org/W1999347963","https://openalex.org/W2001012906","https://openalex.org/W2005747738","https://openalex.org/W2013726100","https://openalex.org/W2028826413","https://openalex.org/W2030026256","https://openalex.org/W2031583623","https://openalex.org/W2045513654","https://openalex.org/W2063034817","https://openalex.org/W2063092201","https://openalex.org/W2063216482","https://openalex.org/W2064258134","https://openalex.org/W2065989745","https://openalex.org/W2072634710","https://openalex.org/W2074570440","https://openalex.org/W2076639450","https://openalex.org/W2080711919","https://openalex.org/W2087574732","https://openalex.org/W2096994057","https://openalex.org/W2097029677","https://openalex.org/W2101444664","https://openalex.org/W2102983156","https://openalex.org/W2111251513","https://openalex.org/W2119821739","https://openalex.org/W2121723608","https://openalex.org/W2123157758","https://openalex.org/W2125055259","https://openalex.org/W2132549764","https://openalex.org/W2133138357","https://openalex.org/W2133167066","https://openalex.org/W2137614677","https://openalex.org/W2139298510","https://openalex.org/W2142873050","https://openalex.org/W2144553406","https://openalex.org/W2145427519","https://openalex.org/W2148219066","https://openalex.org/W2149310258","https://openalex.org/W2167467747","https://openalex.org/W2608702473","https://openalex.org/W2911964244"],"related_works":["https://openalex.org/W2912290813","https://openalex.org/W2082707830","https://openalex.org/W2099982459","https://openalex.org/W1982038138","https://openalex.org/W2010825547","https://openalex.org/W2045131140","https://openalex.org/W2109298101","https://openalex.org/W2159860826","https://openalex.org/W2133294187","https://openalex.org/W4390876228"],"abstract_inverted_index":{"Our":[0],"model":[1],"on":[2],"PDZ":[3,38],"interaction":[4],"dataset":[5],"shows":[6],"that":[7],"our":[8],"approach":[9],"produces":[10],"encouraging":[11],"results.":[12],"The":[13],"method":[14],"can":[15],"be":[16],"further":[17],"used":[18],"as":[19],"a":[20],"virtual":[21],"screening":[22],"technique":[23],"to":[24],"reduce":[25],"the":[26],"search":[27],"space":[28],"for":[29],"putative":[30],"candidate":[31],"target":[32],"proteins":[33],"and":[34],"drug-like":[35],"molecules":[36],"of":[37],"domains.":[39]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":7}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
