{"id":"https://openalex.org/W2735576751","doi":"https://doi.org/10.1186/s12859-017-1755-0","title":"An efficient algorithm for improving structure-based prediction of transcription factor binding sites","display_name":"An efficient algorithm for improving structure-based prediction of transcription factor binding sites","publication_year":2017,"publication_date":"2017-07-17","ids":{"openalex":"https://openalex.org/W2735576751","doi":"https://doi.org/10.1186/s12859-017-1755-0","mag":"2735576751","pmid":"https://pubmed.ncbi.nlm.nih.gov/28715997"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1755-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1755-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1755-0","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/track/pdf/10.1186/s12859-017-1755-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059749354","display_name":"Alvin Farrel","orcid":"https://orcid.org/0000-0003-1087-9840"},"institutions":[{"id":"https://openalex.org/I102149020","display_name":"University of North Carolina at Charlotte","ror":"https://ror.org/04dawnj30","country_code":"US","type":"education","lineage":["https://openalex.org/I102149020"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alvin Farrel","raw_affiliation_strings":["Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA","institution_ids":["https://openalex.org/I102149020"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103170888","display_name":"Jun\u2010tao Guo","orcid":"https://orcid.org/0000-0001-5949-8948"},"institutions":[{"id":"https://openalex.org/I102149020","display_name":"University of North Carolina at Charlotte","ror":"https://ror.org/04dawnj30","country_code":"US","type":"education","lineage":["https://openalex.org/I102149020"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jun-tao Guo","raw_affiliation_strings":["Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA. jguo4@uncc.edu","Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA"],"raw_orcid":"https://orcid.org/0000-0001-5949-8948","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA. jguo4@uncc.edu","institution_ids":["https://openalex.org/I102149020"]},{"raw_affiliation_string":"Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA","institution_ids":["https://openalex.org/I102149020"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5103170888"],"corresponding_institution_ids":["https://openalex.org/I102149020"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.5067,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.62921852,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"18","issue":"1","first_page":"342","last_page":"342"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8385000228881836,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8385000228881836,"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":0.04520000144839287,"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":0.03959999978542328,"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":0.6448255181312561},{"id":"https://openalex.org/keywords/pentamer","display_name":"Pentamer","score":0.6177324652671814},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.6117100119590759},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5835016965866089},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5607187747955322},{"id":"https://openalex.org/keywords/binding-energy","display_name":"Binding energy","score":0.5088598728179932},{"id":"https://openalex.org/keywords/stacking","display_name":"Stacking","score":0.4735742509365082},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.39460301399230957},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3790636360645294},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34289079904556274},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3303448259830475},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2449202537536621},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.23193228244781494},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.20757654309272766},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14806851744651794}],"concepts":[{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.6448255181312561},{"id":"https://openalex.org/C2777331810","wikidata":"https://www.wikidata.org/wiki/Q3374897","display_name":"Pentamer","level":2,"score":0.6177324652671814},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6117100119590759},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5835016965866089},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5607187747955322},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.5088598728179932},{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.4735742509365082},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.39460301399230957},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3790636360645294},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34289079904556274},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3303448259830475},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2449202537536621},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.23193228244781494},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.20757654309272766},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14806851744651794},{"id":"https://openalex.org/C185544564","wikidata":"https://www.wikidata.org/wiki/Q81197","display_name":"Nuclear physics","level":1,"score":0.0},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":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":"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":"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":"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-017-1755-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1755-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1755-0","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:28715997","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28715997","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:pubmedcentral.nih.gov:5514533","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5514533","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 Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:693456a325ce4620a5a015215c7f7f1e","is_oa":false,"landing_page_url":"https://doaj.org/article/693456a325ce4620a5a015215c7f7f1e","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 18, Iss 1, Pp 1-11 (2017)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-1755-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1755-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1755-0","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":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.9100000262260437}],"awards":[{"id":"https://openalex.org/G1208175815","display_name":"Collaborative Research: ABI Innovation: Towards high performance flexible transcription factor-DNA docking","funder_award_id":"1356459","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3586178202","display_name":"Structural Features of Specificity in Protein-DNA Recognition","funder_award_id":"1r15gm110618-01a1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5212890528","display_name":null,"funder_award_id":"R15GM110618","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8032275666","display_name":null,"funder_award_id":"DBI1356459","funder_id":"https://openalex.org/F4320332167","funder_display_name":"Directorate for Biological Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2735576751.pdf","grobid_xml":"https://content.openalex.org/works/W2735576751.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1501210482","https://openalex.org/W1672416630","https://openalex.org/W1833766276","https://openalex.org/W1900337607","https://openalex.org/W1969234006","https://openalex.org/W1970663985","https://openalex.org/W1976579857","https://openalex.org/W1977312774","https://openalex.org/W1977741397","https://openalex.org/W1980722147","https://openalex.org/W1990893875","https://openalex.org/W1994904124","https://openalex.org/W1996261696","https://openalex.org/W1998508434","https://openalex.org/W2002964220","https://openalex.org/W2011282682","https://openalex.org/W2020542137","https://openalex.org/W2022736304","https://openalex.org/W2026395206","https://openalex.org/W2037099334","https://openalex.org/W2041877620","https://openalex.org/W2042303986","https://openalex.org/W2054525948","https://openalex.org/W2069520341","https://openalex.org/W2071962674","https://openalex.org/W2074645168","https://openalex.org/W2074718022","https://openalex.org/W2076556722","https://openalex.org/W2080407755","https://openalex.org/W2085497102","https://openalex.org/W2087058596","https://openalex.org/W2093547815","https://openalex.org/W2098134392","https://openalex.org/W2098312592","https://openalex.org/W2101481219","https://openalex.org/W2102952393","https://openalex.org/W2111826500","https://openalex.org/W2115339329","https://openalex.org/W2123217482","https://openalex.org/W2128937741","https://openalex.org/W2132629607","https://openalex.org/W2134156588","https://openalex.org/W2140405765","https://openalex.org/W2143495231","https://openalex.org/W2145218186","https://openalex.org/W2154106236","https://openalex.org/W2158266834","https://openalex.org/W2161652323","https://openalex.org/W2169837652","https://openalex.org/W2172194625","https://openalex.org/W2304402346","https://openalex.org/W2420058376","https://openalex.org/W2587481461"],"related_works":["https://openalex.org/W2914943284","https://openalex.org/W2036927633","https://openalex.org/W2153561273","https://openalex.org/W2067561164","https://openalex.org/W2152664145","https://openalex.org/W2079197459","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W4233525429","https://openalex.org/W2090848290"],"abstract_inverted_index":{"BACKGROUND:":[0],"Gene":[1],"expression":[2],"is":[3,70,127,222],"regulated":[4],"by":[5,101],"transcription":[6,18,44,117,137,187,229],"factors":[7,19],"binding":[8,46,83,90,104,119,125,162,189,201,231],"to":[9,75,85],"specific":[10],"target":[11],"DNA":[12,103,124],"sites.":[13,91,202],"Understanding":[14],"how":[15],"and":[16,59,154,171,193,209,216],"where":[17],"bind":[20],"at":[21],"genome":[22],"scale":[23],"represents":[24],"an":[25,49,97],"essential":[26],"step":[27],"toward":[28],"our":[29,219],"understanding":[30],"of":[31,43,82],"gene":[32],"regulation":[33],"networks.":[34],"Previously":[35],"we":[36,95,149],"developed":[37,150],"a":[38,55,111,181],"structure-based":[39,228],"method":[40,66,226],"for":[41,88,116,135,160,199,227],"prediction":[42,191],"factor":[45,118,188,230],"sites":[47,232],"using":[48],"integrative":[50,113,183],"energy":[51,62,114,184,211],"function":[52,115,185,212],"that":[53,168],"combines":[54],"knowledge-based":[56],"multibody":[57],"potential":[58],"two":[60,151],"atomic":[61],"terms.":[63],"While":[64],"the":[65,76,80,143,175,223],"performs":[67],"well,":[68],"it":[69],"not":[71],"computationally":[72],"efficient":[73,98],"due":[74],"exponential":[77],"increase":[78],"in":[79,174],"number":[81],"sequences":[84,105],"be":[86],"evaluated":[87],"longer":[89,200],"In":[92],"this":[93,221],"paper,":[94],"present":[96],"pentamer":[99,147,177,207],"algorithm":[100,208],"splitting":[102],"into":[106,129],"overlapping":[107,130,146],"fragments":[108],"along":[109,179],"with":[110,180],"simplified":[112,182,210],"site":[120,190],"prediction.":[121,164,233],"RESULTS:":[122],"A":[123],"sequence":[126],"split":[128],"pentamers":[131],"(5":[132],"base":[133],"pairs)":[134],"calculating":[136],"factor-pentamer":[138],"interaction":[139],"energy.":[140],"To":[141,218],"combine":[142],"results":[144,166],"from":[145],"scores,":[148],"methods,":[152],"Kmer-Sum":[153,170],"PWM":[155,172],"(Position":[156],"Weight":[157],"Matrix)":[158],"stacking,":[159],"full-length":[161],"motif":[163],"Our":[165,204],"show":[167],"both":[169,214],"stacking":[173],"new":[176,205],"approach":[178],"improved":[186],"accuracy":[192],"dramatically":[194],"reduced":[195],"computation":[196],"time,":[197],"especially":[198],"CONCLUSION:":[203],"fragment-based":[206,225],"improve":[213],"efficiency":[215],"accuracy.":[217],"knowledge,":[220],"first":[224]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
