{"id":"https://openalex.org/W2080104767","doi":"https://doi.org/10.1007/s10822-014-9828-x","title":"Role of indirect readout mechanism in TATA box binding protein\u2013DNA interaction","display_name":"Role of indirect readout mechanism in TATA box binding protein\u2013DNA interaction","publication_year":2015,"publication_date":"2015-01-09","ids":{"openalex":"https://openalex.org/W2080104767","doi":"https://doi.org/10.1007/s10822-014-9828-x","mag":"2080104767","pmid":"https://pubmed.ncbi.nlm.nih.gov/25575717"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-014-9828-x","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-014-9828-x","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","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/A5011085880","display_name":"Manas Mondal","orcid":"https://orcid.org/0000-0002-3919-539X"},"institutions":[{"id":"https://openalex.org/I16019930","display_name":"Saha Institute of Nuclear Physics","ror":"https://ror.org/0491yz035","country_code":"IN","type":"facility","lineage":["https://openalex.org/I16019930"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Manas Mondal","raw_affiliation_strings":["Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","Computational Science Division, Saha Institute of Nuclear Physics Kolkata, India"],"affiliations":[{"raw_affiliation_string":"Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","institution_ids":["https://openalex.org/I16019930"]},{"raw_affiliation_string":"Computational Science Division, Saha Institute of Nuclear Physics Kolkata, India","institution_ids":["https://openalex.org/I16019930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036565022","display_name":"Devapriya Choudhury","orcid":"https://orcid.org/0000-0001-6779-9425"},"institutions":[{"id":"https://openalex.org/I152429107","display_name":"Jawaharlal Nehru University","ror":"https://ror.org/0567v8t28","country_code":"IN","type":"education","lineage":["https://openalex.org/I152429107"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Devapriya Choudhury","raw_affiliation_strings":["School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India","School of Biotechnology, Jawaharlal Nehru University, New Delhi, India"],"affiliations":[{"raw_affiliation_string":"School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India","institution_ids":["https://openalex.org/I152429107"]},{"raw_affiliation_string":"School of Biotechnology, Jawaharlal Nehru University, New Delhi, India","institution_ids":["https://openalex.org/I152429107"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058124024","display_name":"J. Chakrabarti","orcid":"https://orcid.org/0000-0003-0753-3259"},"institutions":[{"id":"https://openalex.org/I76587968","display_name":"Bose (United States)","ror":"https://ror.org/0427k1a73","country_code":"US","type":"company","lineage":["https://openalex.org/I76587968"]},{"id":"https://openalex.org/I77430839","display_name":"S.N. Bose National Centre for Basic Sciences","ror":"https://ror.org/00kz6qq24","country_code":"IN","type":"facility","lineage":["https://openalex.org/I77430839"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"Jaydeb Chakrabarti","raw_affiliation_strings":["S.N. Bose National Center for Basic Sciences, Sector III, Salt Lake, Kolkata, 700098, India","S. N. Bose National Center for Basic Sciences,Kolkata,India"],"affiliations":[{"raw_affiliation_string":"S.N. Bose National Center for Basic Sciences, Sector III, Salt Lake, Kolkata, 700098, India","institution_ids":["https://openalex.org/I77430839"]},{"raw_affiliation_string":"S. N. Bose National Center for Basic Sciences,Kolkata,India","institution_ids":["https://openalex.org/I76587968"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051389777","display_name":"Dhananjay Bhattacharyya","orcid":"https://orcid.org/0000-0001-9227-6490"},"institutions":[{"id":"https://openalex.org/I16019930","display_name":"Saha Institute of Nuclear Physics","ror":"https://ror.org/0491yz035","country_code":"IN","type":"facility","lineage":["https://openalex.org/I16019930"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Dhananjay Bhattacharyya","raw_affiliation_strings":["Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","Computational Science Division, Saha Institute of Nuclear Physics Kolkata, India"],"affiliations":[{"raw_affiliation_string":"Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","institution_ids":["https://openalex.org/I16019930"]},{"raw_affiliation_string":"Computational Science Division, Saha Institute of Nuclear Physics Kolkata, India","institution_ids":["https://openalex.org/I16019930"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5011085880"],"corresponding_institution_ids":["https://openalex.org/I16019930"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":0.2968,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.61412863,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"29","issue":"3","first_page":"283","last_page":"295"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998000264167786,"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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9991000294685364,"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":0.6805444955825806},{"id":"https://openalex.org/keywords/tata-box","display_name":"TATA box","score":0.6781002879142761},{"id":"https://openalex.org/keywords/protein\u2013dna-interaction","display_name":"Protein\u2013DNA interaction","score":0.5820574760437012},{"id":"https://openalex.org/keywords/hmg-box","display_name":"HMG-box","score":0.5313675403594971},{"id":"https://openalex.org/keywords/tata-binding-protein","display_name":"TATA-binding protein","score":0.5203697085380554},{"id":"https://openalex.org/keywords/dna-clamp","display_name":"DNA clamp","score":0.4757899045944214},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.46231019496917725},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.4187277853488922},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41480231285095215},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.41303202509880066},{"id":"https://openalex.org/keywords/molecular-biology","display_name":"Molecular biology","score":0.35020673274993896},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.33830660581588745},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2983058989048004},{"id":"https://openalex.org/keywords/dna-binding-protein","display_name":"DNA-binding protein","score":0.2923567295074463},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.17792287468910217},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.14657625555992126},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.14598852396011353},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.11075833439826965}],"concepts":[{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.6805444955825806},{"id":"https://openalex.org/C65888428","wikidata":"https://www.wikidata.org/wiki/Q1413955","display_name":"TATA box","level":5,"score":0.6781002879142761},{"id":"https://openalex.org/C32010083","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"Protein\u2013DNA interaction","level":5,"score":0.5820574760437012},{"id":"https://openalex.org/C5179208","wikidata":"https://www.wikidata.org/wiki/Q3782057","display_name":"HMG-box","level":5,"score":0.5313675403594971},{"id":"https://openalex.org/C2780055153","wikidata":"https://www.wikidata.org/wiki/Q14878262","display_name":"TATA-binding protein","level":5,"score":0.5203697085380554},{"id":"https://openalex.org/C31254050","wikidata":"https://www.wikidata.org/wiki/Q22328799","display_name":"DNA clamp","level":5,"score":0.4757899045944214},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.46231019496917725},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.4187277853488922},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41480231285095215},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.41303202509880066},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.35020673274993896},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.33830660581588745},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2983058989048004},{"id":"https://openalex.org/C94966510","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"DNA-binding protein","level":4,"score":0.2923567295074463},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17792287468910217},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.14657625555992126},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.14598852396011353},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.11075833439826965},{"id":"https://openalex.org/C156719811","wikidata":"https://www.wikidata.org/wiki/Q28774","display_name":"Reverse transcriptase","level":4,"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":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016385","descriptor_name":"TATA Box","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016385","descriptor_name":"TATA Box","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016385","descriptor_name":"TATA Box","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035181","descriptor_name":"TATA-Box Binding Protein","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035181","descriptor_name":"TATA-Box Binding Protein","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035181","descriptor_name":"TATA-Box Binding Protein","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035181","descriptor_name":"TATA-Box Binding Protein","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D035181","descriptor_name":"TATA-Box Binding Protein","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D035181","descriptor_name":"TATA-Box Binding Protein","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-014-9828-x","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-014-9828-x","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:25575717","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25575717","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 computer-aided molecular design","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":69,"referenced_works":["https://openalex.org/W1494314295","https://openalex.org/W1577890972","https://openalex.org/W1833880294","https://openalex.org/W1884135206","https://openalex.org/W1967737979","https://openalex.org/W1968185864","https://openalex.org/W1971389719","https://openalex.org/W1982234546","https://openalex.org/W1982338804","https://openalex.org/W1982404448","https://openalex.org/W1986697554","https://openalex.org/W1988241218","https://openalex.org/W1990706450","https://openalex.org/W1992787746","https://openalex.org/W1999597013","https://openalex.org/W2004912100","https://openalex.org/W2008708467","https://openalex.org/W2008925358","https://openalex.org/W2010004274","https://openalex.org/W2016841933","https://openalex.org/W2020069709","https://openalex.org/W2020830418","https://openalex.org/W2023295965","https://openalex.org/W2027281272","https://openalex.org/W2027659013","https://openalex.org/W2032183039","https://openalex.org/W2032864324","https://openalex.org/W2035797443","https://openalex.org/W2036000659","https://openalex.org/W2037099334","https://openalex.org/W2040007286","https://openalex.org/W2042426030","https://openalex.org/W2046943018","https://openalex.org/W2048562981","https://openalex.org/W2052610951","https://openalex.org/W2066099672","https://openalex.org/W2066962978","https://openalex.org/W2067924339","https://openalex.org/W2071656198","https://openalex.org/W2073535845","https://openalex.org/W2084165318","https://openalex.org/W2094767710","https://openalex.org/W2094795801","https://openalex.org/W2094829545","https://openalex.org/W2095150400","https://openalex.org/W2096929343","https://openalex.org/W2099001053","https://openalex.org/W2103815459","https://openalex.org/W2105454016","https://openalex.org/W2105463149","https://openalex.org/W2108147660","https://openalex.org/W2117314105","https://openalex.org/W2119588582","https://openalex.org/W2122199548","https://openalex.org/W2122932522","https://openalex.org/W2123529526","https://openalex.org/W2127382372","https://openalex.org/W2130479394","https://openalex.org/W2136729627","https://openalex.org/W2139064328","https://openalex.org/W2147466870","https://openalex.org/W2154319440","https://openalex.org/W2155601193","https://openalex.org/W2156736748","https://openalex.org/W2156909690","https://openalex.org/W2157459448","https://openalex.org/W4234971400","https://openalex.org/W4250241002","https://openalex.org/W4254093784"],"related_works":["https://openalex.org/W2141001285","https://openalex.org/W2019511508","https://openalex.org/W2095914699","https://openalex.org/W2016686206","https://openalex.org/W2095487472","https://openalex.org/W2444470526","https://openalex.org/W4206974957","https://openalex.org/W2166464288","https://openalex.org/W2085443893","https://openalex.org/W2080104767"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
