{"id":"https://openalex.org/W2153543220","doi":"https://doi.org/10.1186/1752-0509-8-s4-s10","title":"A graph kernel method for DNA-binding site prediction","display_name":"A graph kernel method for DNA-binding site prediction","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2153543220","doi":"https://doi.org/10.1186/1752-0509-8-s4-s10","mag":"2153543220","pmid":"https://pubmed.ncbi.nlm.nih.gov/25521807"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-8-s4-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-8-s4-s10","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-S4-S10","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-S4-S10","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100871727","display_name":"Changhui Yan","orcid":"https://orcid.org/0000-0003-3048-8628"},"institutions":[{"id":"https://openalex.org/I57328836","display_name":"North Dakota State University","ror":"https://ror.org/05h1bnb22","country_code":"US","type":"education","lineage":["https://openalex.org/I57328836"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Changhui Yan","raw_affiliation_strings":["Department of Computer Science, North Dakota State University, Fargo, ND, 58108, USA","Department of Computer Science, North Dakota State University, Fargo, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, North Dakota State University, Fargo, ND, 58108, USA","institution_ids":["https://openalex.org/I57328836"]},{"raw_affiliation_string":"Department of Computer Science, North Dakota State University, Fargo, USA","institution_ids":["https://openalex.org/I57328836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005662495","display_name":"Yingfeng Wang","orcid":"https://orcid.org/0000-0002-3715-5124"},"institutions":[{"id":"https://openalex.org/I121980950","display_name":"Utah State University","ror":"https://ror.org/00h6set76","country_code":"US","type":"education","lineage":["https://openalex.org/I121980950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yingfeng Wang","raw_affiliation_strings":["Department of Computer Science, Utah State University, Logan, UT, 84322, USA","Department of Computer Science, Utah State University, Logan, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Utah State University, Logan, UT, 84322, USA","institution_ids":["https://openalex.org/I121980950"]},{"raw_affiliation_string":"Department of Computer Science, Utah State University, Logan, USA","institution_ids":["https://openalex.org/I121980950"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100871727"],"corresponding_institution_ids":["https://openalex.org/I57328836"],"apc_list":null,"apc_paid":null,"fwci":0.8537,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.73635372,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"8","issue":"Suppl 4","first_page":"S10","last_page":"S10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.49459999799728394,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.49459999799728394,"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":0.2962999939918518,"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":0.03669999912381172,"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","display_name":"DNA","score":0.5834645628929138},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5770957469940186},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5689970850944519},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.5075939893722534},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4870801270008087},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45563238859176636},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.44825172424316406},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.44475623965263367},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3304794430732727},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23259159922599792},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20023155212402344},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11354568600654602},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09813961386680603}],"concepts":[{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5834645628929138},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5770957469940186},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5689970850944519},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.5075939893722534},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4870801270008087},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45563238859176636},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.44825172424316406},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.44475623965263367},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3304794430732727},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23259159922599792},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20023155212402344},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11354568600654602},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09813961386680603},{"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","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}],"locations_count":3,"locations":[{"id":"doi:10.1186/1752-0509-8-s4-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-8-s4-s10","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-S4-S10","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},{"id":"pmid:25521807","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25521807","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 systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4290685","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4290685","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-8-s4-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-8-s4-s10","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-S4-S10","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G131625746","display_name":"II-New: ABC-A Biology Cloud","funder_award_id":"1305175","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G459088676","display_name":"ABI Innovation: Computational methods for macromolecular binding analysis","funder_award_id":"1262265","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2153543220.pdf","grobid_xml":"https://content.openalex.org/works/W2153543220.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1491553314","https://openalex.org/W1543773936","https://openalex.org/W1965582988","https://openalex.org/W1971894358","https://openalex.org/W2005423065","https://openalex.org/W2017727500","https://openalex.org/W2048586347","https://openalex.org/W2051808158","https://openalex.org/W2057664120","https://openalex.org/W2089716128","https://openalex.org/W2096986143","https://openalex.org/W2099254366","https://openalex.org/W2099438806","https://openalex.org/W2102864597","https://openalex.org/W2128533758","https://openalex.org/W2130479394","https://openalex.org/W2141149420","https://openalex.org/W2144347309","https://openalex.org/W2147286743","https://openalex.org/W2149640119","https://openalex.org/W2152116196","https://openalex.org/W2153153865","https://openalex.org/W2153543220","https://openalex.org/W2158714788","https://openalex.org/W2166248605","https://openalex.org/W4245936780"],"related_works":["https://openalex.org/W2763663556","https://openalex.org/W2036927633","https://openalex.org/W2153561273","https://openalex.org/W2152664145","https://openalex.org/W2079197459","https://openalex.org/W2067561164","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W4233525429","https://openalex.org/W2090848290"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein-DNA":[1],"interactions":[2],"play":[3],"important":[4],"roles":[5],"in":[6,155,173],"many":[7],"biological":[8],"processes.":[9],"Computational":[10],"methods":[11,147],"that":[12,149],"can":[13],"accurately":[14],"predict":[15],"DNA-binding":[16,37,81,112,119,142,157,228],"sites":[17,38,113,158,229],"on":[18,24,39,76,94,114,159,197],"proteins":[19],"will":[20],"greatly":[21],"expedite":[22],"research":[23],"problems":[25],"involving":[26],"protein-DNA":[27,100],"interactions.":[28],"RESULTS:":[29],"This":[30],"paper":[31],"presents":[32],"a":[33,53,95,223],"method":[34,43,56,88,107,135,152,165,204,210,225],"for":[35,217,226],"predicting":[36,156,227],"protein":[40,45],"structures.":[41],"The":[42,86,163],"represents":[44],"surface":[46,65],"patches":[47,82],"using":[48,102],"labeled":[49],"graphs":[50,167,207],"and":[51,83],"uses":[52,166],"graph":[54],"kernel":[55,203],"to":[57,69,79,110,168,205],"calculate":[58],"the":[59,106,124,127,133,138,141,150,170,174,186,192,198,208,213],"similarities":[60,78],"between":[61],"graphs.":[62],"A":[63],"new":[64],"patch":[66,74,130],"is":[67],"predicted":[68,131],"be":[70],"interface":[71],"or":[72],"non-interface":[73],"based":[75],"its":[77],"known":[80],"non-DNA-binding":[84],"patches.":[85],"proposed":[87,134,151,164,209],"achieved":[89],"high":[90],"accuracy":[91],"when":[92],"tested":[93],"representative":[96],"set":[97],"of":[98,118,123,140,188,195],"146":[99],"complexes":[101],"leave-one-out":[103],"cross-validation.":[104],"Then,":[105],"was":[108,153],"applied":[109],"identify":[111],"13":[115],"unbound":[116,125,160],"structures":[117],"proteins.":[120,161,199],"In":[121],"each":[122],"structure,":[126],"top":[128],"1":[129],"by":[132],"precisely":[136],"indicated":[137],"location":[139],"site.":[143],"Comparisons":[144],"with":[145,180],"other":[146,181],"showed":[148],"competitive":[154,224],"CONCLUSIONS:":[162],"encode":[169],"feature's":[171],"distribution":[172,194],"3-dimensional":[175],"(3D)":[176],"space.":[177],"Thus,":[178],"compared":[179],"vector-based":[182],"methods,":[183],"it":[184],"has":[185],"advantage":[187],"taking":[189],"into":[190],"account":[191],"spatial":[193],"features":[196],"Using":[200],"an":[201],"efficient":[202],"compare":[206],"also":[211],"avoids":[212],"demanding":[214],"computations":[215],"required":[216],"3D":[218],"objects":[219],"comparison.":[220],"It":[221],"provides":[222],"without":[230],"requiring":[231],"structure":[232],"alignment.":[233]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}