{"id":"https://openalex.org/W6958486605","doi":"https://doi.org/10.6094/unifr/10177","title":"In Silico Prediction of Modular Domain-Peptide Interactions","display_name":"In Silico Prediction of Modular Domain-Peptide Interactions","publication_year":2015,"publication_date":"2015-01-01","ids":{"openalex":"https://openalex.org/W6958486605","doi":"https://doi.org/10.6094/unifr/10177"},"language":"en","primary_location":{"id":"pmh:oai:freidok.uni-freiburg.de:10177","is_oa":false,"landing_page_url":"https://freidok.uni-freiburg.de/data/10177","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"doctoral_thesis"},"type":"other","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.6094/unifr/10177","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Kundu, Kousik","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Kundu, Kousik","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.7631000280380249},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.7552000284194946},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4607999920845032},{"id":"https://openalex.org/keywords/modularity","display_name":"Modularity (biology)","score":0.45100000500679016},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.4343999922275543},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4004000127315521},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.366100013256073},{"id":"https://openalex.org/keywords/pdz-domain","display_name":"PDZ domain","score":0.3215000033378601}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7631000280380249},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.7552000284194946},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7028999924659729},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6385999917984009},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4607999920845032},{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.45100000500679016},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.4343999922275543},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4004000127315521},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38260000944137573},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.366100013256073},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32679998874664307},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32269999384880066},{"id":"https://openalex.org/C154428179","wikidata":"https://www.wikidata.org/wiki/Q24721050","display_name":"PDZ domain","level":2,"score":0.3215000033378601},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.3149999976158142},{"id":"https://openalex.org/C197153747","wikidata":"https://www.wikidata.org/wiki/Q24780316","display_name":"SH2 domain","level":4,"score":0.29350000619888306},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.28790000081062317},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.28630000352859497},{"id":"https://openalex.org/C70636015","wikidata":"https://www.wikidata.org/wiki/Q4300350","display_name":"Molecular biophysics","level":2,"score":0.2816999852657318},{"id":"https://openalex.org/C122280245","wikidata":"https://www.wikidata.org/wiki/Q620622","display_name":"Kernel method","level":3,"score":0.26829999685287476},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.26829999685287476},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2662999927997589},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26030001044273376},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.2558000087738037},{"id":"https://openalex.org/C61727976","wikidata":"https://www.wikidata.org/wiki/Q751748","display_name":"Epistasis","level":3,"score":0.2556999921798706}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:freidok.uni-freiburg.de:10177","is_oa":false,"landing_page_url":"https://freidok.uni-freiburg.de/data/10177","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"doctoral_thesis"},{"id":"doi:10.6094/unifr/10177","is_oa":true,"landing_page_url":"https://doi.org/10.6094/unifr/10177","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.6094/unifr/10177","is_oa":true,"landing_page_url":"https://doi.org/10.6094/unifr/10177","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Protein-protein":[0],"interactions":[1,226],"(PPIs)":[2],"are":[3,34,44,151,206,268,298],"one":[4],"of":[5,48,75,106,109,120,125,130,137,159,171,201,216,263,293,315,327,342,350,371,389,395,421,471,481,557,565,588,635,662,671,678],"the":[6,69,103,116,134,142,156,169,189,213,243,261,272,281,291,302,312,320,324,328,340,348,368,372,382,387,431,445,468,476,528,533,554,558,562,586,632,641,655,660,668,676],"most":[7],"essential":[8],"cellular":[9,32,87],"processes":[10],"in":[11,31,84,98,122,209,319,659],"eukaryotes":[12],"that":[13,52,150,205,430],"control":[14],"many":[15],"important":[16,46,66],"biological":[17,61],"activities,":[18],"such":[19],"as":[20,522],"signal":[21],"transduction,":[22],"differentiation,":[23],"growth,":[24],"cell":[25],"polarity,":[26],"apoptosis":[27],"etc.":[28],"Many":[29],"PPIs":[30],"signaling":[33],"mediated":[35,227,681],"by":[36,72,228,284,354,437,502],"modular":[37,49,76,110,589,663,679],"protein":[38,50,111],"domains.":[39,424],"Peptide":[40],"recognition":[41],"modules":[42],"(PRMs)":[43],"an":[45,92,286,343,362,439],"subclass":[47],"domains":[51,77,356,397,618],"specifically":[53,78],"recognize":[54],"short":[55],"linear":[56],"peptides":[57,83,352,634],"to":[58,67,80,101,241,270,279,310,338,454,462,552,673],"facilitate":[59],"their":[60,81,126,184,409],"functions.":[62],"Hence,":[63],"it":[64],"is":[65,129,357,451],"understand":[68],"intriguing":[70],"mechanisms":[71],"which":[73,252,322,499,576,612],"hundreds":[74,394],"bind":[79],"target":[82],"a":[85,107,177,358,377,414,419,447,457,495,523,541,545,570],"complex":[86],"environment.":[88],"In":[89,133,212,239,274,386,425,467,561,622],"recent":[90],"years,":[91],"unprecedented":[93],"progress":[94],"has":[95,549],"been":[96,166,550],"made":[97],"high-throughput":[99,144,648],"technologies":[100,145],"describe":[102,141,188,475],"binding":[104,118,157,410,633],"specificities":[105],"number":[108],"domain":[112,432,599,610,680],"families.":[113],"Therefore,":[114],"given":[115],"high":[117],"specificity":[119,158],"PRMs,":[121],"silico":[123],"prediction":[124,170,262,292,587,677],"cognate":[127],"partners":[128],"great":[131],"interest.":[132],"first":[135],"part":[136,215,470,564],"this":[138,217,332,426,472,566,624,652],"thesis,":[139,218,473,567],"we":[140,175,219,276,335,375,392,428,474,539,568,593],"main":[143],"(microarray,":[146],"phage":[147],"display":[148],"etc.)":[149,200],"widely":[152],"used":[153,269,299],"for":[154,168,223,300,380,418,585,601,616,630,675],"defining":[155],"PRMs.":[160],"Currently,":[161,592],"several":[162,489,620],"computational":[163,657],"methods":[164,182,222,247,487,512,629],"have":[165],"published":[167],"domain-peptide":[172,225,590,664],"interactions.":[173,560,591,665,682],"Here,":[174],"provide":[176],"comprehensive":[178,416],"review":[179],"on":[180,408,516],"these":[181,202],"and":[183,236,361,405,412,478,493,508,521,535,572,583,596,603,607],"applications.":[185],"We":[186,484,666],"also":[187],"major":[190,656],"drawbacks":[191],"(e.g.,":[192],"linearity":[193,244],"problem,":[194,197,245],"peptide":[195,345],"alignment":[196,349,364],"data-imbalance":[198,282],"problem":[199,283],"existing":[203,491],"tools":[204,492,579],"successfully":[207],"addressed":[208],"our":[210,246,482,486],"study.":[211],"second":[214],"present":[220],"three":[221,229,578,636],"predicting":[224,631],"diverse":[230,637],"PRM":[231,638],"families":[232,639],"(i.e.,":[233,580],"SH2,":[234],"SH3,":[235],"PDZ":[237,396,423,617],"domain).":[238],"order":[240],"circumvent":[242],"use":[248],"efficient":[249,287,573],"kernel":[250,305,333,449],"functions,":[251],"exploit":[253],"higher-order":[254],"dependencies":[255],"between":[256],"amino":[257,317],"acid":[258,318],"positions.":[259],"For":[260,290,443],"SH2-peptide":[264,455],"interactions,":[265,295,391,456,538],"polynomial":[266],"kernels":[267,297],"train":[271],"classifiers.":[273,303],"addition,":[275],"show":[277,429],"how":[278],"handle":[280],"using":[285,331,438],"semi-supervised":[288,458],"technique.":[289,442],"SH3-peptide":[294],"graph":[296],"training":[301,444,642],"Graph":[304],"feature":[306],"representation":[307],"allows":[308],"us":[309],"include":[311],"physico-chemical":[313],"properties":[314],"each":[316],"peptides,":[321],"increases":[323],"generalization":[325],"capacity":[326],"classifier.":[329,373],"By":[330],"function,":[334],"were":[336,513],"able":[337],"eliminate":[339],"need":[341],"initial":[344],"alignment,":[346],"since":[347],"proline-rich":[351],"targeted":[353],"SH3":[355,604],"hard":[359],"task":[360],"error-prone":[363],"can":[365,434],"severely":[366],"affect":[367],"predictive":[369,524],"performance":[370,479],"Moreover,":[374],"developed":[376],"generative":[378],"approach":[379],"refining":[381],"confidence":[383],"negative":[384,465],"data.":[385,466],"case":[388],"PDZ-peptide":[390],"cluster":[393],"from":[398,646],"different":[399],"organisms,":[400],"i.e.,":[401],"human,":[402],"mouse,":[403],"fly,":[404],"worm,":[406],"based":[407],"specificity,":[411,504],"build":[413],"single":[415,598],"model":[417],"set":[420,670],"multiple":[422,609],"way,":[427],"coverage":[433],"be":[435],"increased":[436],"accurate":[440],"clustering":[441],"classifier,":[446],"Gaussian":[448],"function":[450],"used.":[452],"Similar":[453],"technique":[459],"was":[460,500,644],"applied":[461],"generate":[463],"high-confidence":[464],"third":[469],"applications":[477],"evaluations":[480],"methods.":[483],"compared":[485],"with":[488],"other":[490],"achieved":[494],"much":[496],"higher":[497],"performance,":[498],"measured":[501],"sensitivity,":[503],"precision,":[505],"AUC":[506,509],"PR,":[507],"ROC.":[510],"Our":[511],"further":[514],"evaluated":[515],"various":[517,647],"experimentally":[518],"verified":[519],"datasets":[520],"result,":[525],"they":[526],"outperformed":[527],"state-of-the-art":[529],"approaches.":[530],"To":[531],"uncover":[532],"novel":[534,555],"biologically":[536],"relevant":[537],"performed":[540,551],"genome-wide":[542],"prediction.":[543],"Furthermore,":[544],"term-centric":[546],"enrichment":[547],"analysis":[548],"unveil":[553],"functionalities":[556],"predicted":[559],"last":[563],"introduce":[569],"new":[571],"web":[574],"server,":[575],"contains":[577],"SH2PepInt,":[581],"SH3PepInt,":[582],"PDZPepInt),":[584],"offer":[594,667],"51":[595],"69":[597],"models":[600,672],"SH2":[602],"domains,":[605,615],"respectively,":[606],"43":[608],"models,":[611],"cover":[613],"227":[614],"across":[619],"organisms.":[621],"summary,":[623],"thesis":[625,653],"presents":[626],"machine":[627],"learning":[628],"where":[640],"data":[643],"derived":[645],"experiments.":[649],"Most":[650],"importantly,":[651],"addresses":[654],"challenges":[658],"field":[661],"largest":[669],"date":[674]},"counts_by_year":[],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
