{"id":"https://openalex.org/W2022255311","doi":"https://doi.org/10.1142/s0219720004000569","title":"BINDING MATRIX: A NOVEL APPROACH FOR BINDING SITE RECOGNITION","display_name":"BINDING MATRIX: A NOVEL APPROACH FOR BINDING SITE RECOGNITION","publication_year":2004,"publication_date":"2004-05-27","ids":{"openalex":"https://openalex.org/W2022255311","doi":"https://doi.org/10.1142/s0219720004000569","mag":"2022255311","pmid":"https://pubmed.ncbi.nlm.nih.gov/15297983"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720004000569","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720004000569","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074101757","display_name":"Jan T. Kim","orcid":"https://orcid.org/0000-0001-8539-0666"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"JAN T. KIM","raw_affiliation_strings":["Ratzeburger Allee 160, Geb\u00e4ude 64, D-23538 L\u00fcbeck, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ratzeburger Allee 160, Geb\u00e4ude 64, D-23538 L\u00fcbeck, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068369157","display_name":"Jan E. Gewehr","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"JAN E. GEWEHR","raw_affiliation_strings":["Ratzeburger Allee 160, Geb\u00e4ude 64, D-23538 L\u00fcbeck, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ratzeburger Allee 160, Geb\u00e4ude 64, D-23538 L\u00fcbeck, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014856404","display_name":"Thomas Martinetz","orcid":"https://orcid.org/0000-0002-4539-4475"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"THOMAS MARTINETZ","raw_affiliation_strings":["Ratzeburger Allee 160, Geb\u00e4ude 64, D-23538 L\u00fcbeck, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ratzeburger Allee 160, Geb\u00e4ude 64, D-23538 L\u00fcbeck, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.479,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.61118612,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"02","issue":"02","first_page":"289","last_page":"307"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9987000226974487,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9987000226974487,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9973999857902527,"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/dna-binding-site","display_name":"DNA binding site","score":0.5950952768325806},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.5513519644737244},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.49214619398117065},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4469418525695801},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4260202944278717},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4145314693450928},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37706857919692993},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3738800883293152},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.355424165725708},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3533961772918701},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.33976924419403076},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30425262451171875},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21477696299552917},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13958615064620972},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.12958943843841553}],"concepts":[{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5950952768325806},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.5513519644737244},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.49214619398117065},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4469418525695801},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4260202944278717},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4145314693450928},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37706857919692993},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3738800883293152},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.355424165725708},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3533961772918701},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.33976924419403076},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30425262451171875},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21477696299552917},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13958615064620972},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.12958943843841553},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1142/s0219720004000569","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720004000569","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:15297983","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15297983","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":"Journal of bioinformatics and computational biology","raw_type":null},{"id":"pmh:oai:ueaeprints.uea.ac.uk:22693","is_oa":false,"landing_page_url":"https://ueaeprints.uea.ac.uk/id/eprint/22693/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400384","display_name":"UEA Digital Repository (University of East Anglia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1118541","host_organization_name":"University of East Anglia","host_organization_lineage":["https://openalex.org/I1118541"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.7599999904632568}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1498410508","https://openalex.org/W1552703317","https://openalex.org/W1562374859","https://openalex.org/W1983405741","https://openalex.org/W1988303029","https://openalex.org/W1998300401","https://openalex.org/W2018507982","https://openalex.org/W2031121939","https://openalex.org/W2032548898","https://openalex.org/W2035564383","https://openalex.org/W2057000344","https://openalex.org/W2066562848","https://openalex.org/W2069426496","https://openalex.org/W2074703985","https://openalex.org/W2108190672","https://openalex.org/W2142890842","https://openalex.org/W2146393977","https://openalex.org/W2149769193","https://openalex.org/W2154100003","https://openalex.org/W2158089930","https://openalex.org/W2166277117","https://openalex.org/W2786741601"],"related_works":["https://openalex.org/W2036927633","https://openalex.org/W2152664145","https://openalex.org/W2153561273","https://openalex.org/W2079197459","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W2090848290","https://openalex.org/W2146393977","https://openalex.org/W2122429294","https://openalex.org/W2146517458"],"abstract_inverted_index":{"Recognition":[0],"of":[1,16,23,41,70,100,132,179,199],"protein-DNA":[2],"binding":[3,32,71,85,89,106,126,160,163,181,202],"sites":[4],"in":[5,21,28,65,78,187],"genomic":[6,17],"sequences":[7,134],"is":[8,46,63,86,92,165,173,194],"a":[9,29,52,67,79,154],"crucial":[10],"step":[11],"for":[12,31,147],"discovering":[13],"biological":[14],"functions":[15],"sequences.":[18],"Explosive":[19],"growth":[20],"availability":[22],"sequence":[24,101],"information":[25],"has":[26],"resulted":[27],"demand":[30,50],"site":[33,72],"detection":[34,73],"methods":[35,74],"with":[36,175],"high":[37],"specificity.":[38],"The":[39,129,162],"motivation":[40],"the":[42,98,120,125,159,166,176,206],"work":[43],"presented":[44],"here":[45],"to":[47,118,153,190],"address":[48],"this":[49,141,149],"by":[51,88,124,205],"systematic":[53],"approach":[54,146],"based":[55,105,170],"on":[56],"Maximum":[57],"Likelihood":[58],"Estimation.":[59],"A":[60,143],"general":[61],"framework":[62],"developed":[64],"which":[66,91,116,172],"large":[68],"class":[69],"can":[75,109],"be":[76,110],"described":[77,139],"uniform":[80],"and":[81,135],"consistent":[82,174],"way.":[83],"Protein-DNA":[84],"determined":[87,201],"energy,":[90],"an":[93],"approximately":[94],"linear":[95,114,121,150],"function":[96],"within":[97],"space":[99],"words.":[102,182],"All":[103],"matrix":[104,156,164,169],"word":[107],"detectors":[108],"regarded":[111],"as":[112],"different":[113],"classifiers":[115],"attempt":[117],"estimate":[119],"separation":[122,151],"implied":[123],"energy":[127],"function.":[128],"standard":[130],"approaches":[131],"consensus":[133],"profile":[136],"matrices":[137],"are":[138],"using":[140,196],"framework.":[142],"maximum":[144],"likelihood":[145],"determining":[148],"leads":[152],"novel":[155],"type,":[157],"called":[158],"matrix.":[161],"most":[167],"specific":[168],"classifier":[171],"input":[177],"set":[178],"known":[180],"It":[183],"achieves":[184],"significant":[185],"improvements":[186],"specificity":[188],"compared":[189],"other":[191],"matrices.":[192],"This":[193],"demonstrated":[195],"95":[197],"sets":[198],"experimentally":[200],"words":[203],"provided":[204],"TRANSFAC":[207],"database.":[208]},"counts_by_year":[{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}