{"id":"https://openalex.org/W2420058376","doi":"https://doi.org/10.1093/bioinformatics/btw264","title":"Structure-based prediction of transcription factor binding specificity using an integrative energy function","display_name":"Structure-based prediction of transcription factor binding specificity using an integrative energy function","publication_year":2016,"publication_date":"2016-06-11","ids":{"openalex":"https://openalex.org/W2420058376","doi":"https://doi.org/10.1093/bioinformatics/btw264","mag":"2420058376","pmid":"https://pubmed.ncbi.nlm.nih.gov/27307632"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw264","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw264","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/12/i306/17130126/btw264.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/12/i306/17130126/btw264.pdf","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, Charlotte, NC 28223, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA","institution_ids":["https://openalex.org/I102149020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087271270","display_name":"Jonathan G. Murphy","orcid":"https://orcid.org/0000-0001-6485-5727"},"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":"Jonathan Murphy","raw_affiliation_strings":["Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 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, Charlotte, NC 28223, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA","institution_ids":["https://openalex.org/I102149020"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5103170888"],"corresponding_institution_ids":["https://openalex.org/I102149020"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5665,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.8344765,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"32","issue":"12","first_page":"i306","last_page":"i313"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9995999932289124,"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":0.9986000061035156,"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/transcription-factor","display_name":"Transcription factor","score":0.6458978652954102},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5419865250587463},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4829515814781189},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4752747118473053},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.350149005651474},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32616686820983887},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3130931854248047},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2194085419178009},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11198630928993225}],"concepts":[{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6458978652954102},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5419865250587463},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4829515814781189},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4752747118473053},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.350149005651474},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32616686820983887},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3130931854248047},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2194085419178009},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11198630928993225}],"mesh":[{"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":"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":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw264","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw264","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/12/i306/17130126/btw264.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27307632","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27307632","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/12/i306","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/12/i306","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:4908348","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4908348","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw264","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw264","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/12/i306/17130126/btw264.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8999999761581421,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2420058376.pdf","grobid_xml":"https://content.openalex.org/works/W2420058376.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1964733653","https://openalex.org/W1969234006","https://openalex.org/W1976579857","https://openalex.org/W1977312774","https://openalex.org/W1977741397","https://openalex.org/W1980722147","https://openalex.org/W1986586522","https://openalex.org/W1996261696","https://openalex.org/W1998508434","https://openalex.org/W2009158394","https://openalex.org/W2011282682","https://openalex.org/W2020542137","https://openalex.org/W2026395206","https://openalex.org/W2041877620","https://openalex.org/W2053037206","https://openalex.org/W2067219399","https://openalex.org/W2074645168","https://openalex.org/W2093547815","https://openalex.org/W2098134392","https://openalex.org/W2098312592","https://openalex.org/W2101481219","https://openalex.org/W2102952393","https://openalex.org/W2110281506","https://openalex.org/W2128937741","https://openalex.org/W2130479394","https://openalex.org/W2132082217","https://openalex.org/W2132629607","https://openalex.org/W2137154596","https://openalex.org/W2137704807","https://openalex.org/W2140405765","https://openalex.org/W2142134255","https://openalex.org/W2149769193","https://openalex.org/W2150308082","https://openalex.org/W2153119245","https://openalex.org/W2158266834","https://openalex.org/W2161062388","https://openalex.org/W2161652323","https://openalex.org/W2166162901","https://openalex.org/W2169837652","https://openalex.org/W2171777347","https://openalex.org/W2185259716","https://openalex.org/W2346035106","https://openalex.org/W2885727518","https://openalex.org/W4211054902","https://openalex.org/W4211208250","https://openalex.org/W4254829742","https://openalex.org/W6682301761"],"related_works":["https://openalex.org/W2772917594","https://openalex.org/W4306742369","https://openalex.org/W4303457083","https://openalex.org/W4376623224","https://openalex.org/W2951359407","https://openalex.org/W2124566234","https://openalex.org/W3136979370","https://openalex.org/W2036807459","https://openalex.org/W2058170566","https://openalex.org/W2904126538"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
