{"id":"https://openalex.org/W2977750995","doi":"https://doi.org/10.1021/acs.jcim.9b00685","title":"Flexibility of the Binding Regions of a Protein\u2013DNA Complex and the Structure and Ordering of Interfacial Water","display_name":"Flexibility of the Binding Regions of a Protein\u2013DNA Complex and the Structure and Ordering of Interfacial Water","publication_year":2019,"publication_date":"2019-10-03","ids":{"openalex":"https://openalex.org/W2977750995","doi":"https://doi.org/10.1021/acs.jcim.9b00685","mag":"2977750995","pmid":"https://pubmed.ncbi.nlm.nih.gov/31580657"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00685","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00685","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","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/A5078521338","display_name":"Sandip Mondal","orcid":"https://orcid.org/0000-0002-0654-6376"},"institutions":[{"id":"https://openalex.org/I145894827","display_name":"Indian Institute of Technology Kharagpur","ror":"https://ror.org/03w5sq511","country_code":"IN","type":"education","lineage":["https://openalex.org/I145894827"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sandip Mondal","raw_affiliation_strings":["Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India"],"raw_orcid":"https://orcid.org/0000-0002-0654-6376","affiliations":[{"raw_affiliation_string":"Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India","institution_ids":["https://openalex.org/I145894827"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051434187","display_name":"Sanjoy Bandyopadhyay","orcid":"https://orcid.org/0000-0002-3267-6326"},"institutions":[{"id":"https://openalex.org/I145894827","display_name":"Indian Institute of Technology Kharagpur","ror":"https://ror.org/03w5sq511","country_code":"IN","type":"education","lineage":["https://openalex.org/I145894827"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Sanjoy Bandyopadhyay","raw_affiliation_strings":["Molecular Modeling Laboratory, Department of Chemistry \u00a0and\u00a0 Centre for Computational and Data Sciences, Indian Institute of Technology, Kharagpur 721302, India"],"raw_orcid":"https://orcid.org/0000-0002-3267-6326","affiliations":[{"raw_affiliation_string":"Molecular Modeling Laboratory, Department of Chemistry \u00a0and\u00a0 Centre for Computational and Data Sciences, Indian Institute of Technology, Kharagpur 721302, India","institution_ids":["https://openalex.org/I145894827"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5051434187"],"corresponding_institution_ids":["https://openalex.org/I145894827"],"apc_list":null,"apc_paid":null,"fwci":0.4274,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.62682772,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"59","issue":"10","first_page":"4427","last_page":"4437"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9966999888420105,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9966999888420105,"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":0.9957000017166138,"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":0.9796000123023987,"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":0.7867209911346436},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.6819040775299072},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5738307237625122},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5250915288925171},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.5085016489028931},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.4987931251525879},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.454471230506897},{"id":"https://openalex.org/keywords/repressor","display_name":"Repressor","score":0.45264437794685364},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.22504833340644836},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.19681748747825623},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14912760257720947},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07543963193893433},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.07525560259819031}],"concepts":[{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.7867209911346436},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.6819040775299072},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5738307237625122},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5250915288925171},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.5085016489028931},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4987931251525879},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.454471230506897},{"id":"https://openalex.org/C158448853","wikidata":"https://www.wikidata.org/wiki/Q425218","display_name":"Repressor","level":4,"score":0.45264437794685364},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.22504833340644836},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.19681748747825623},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14912760257720947},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07543963193893433},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.07525560259819031},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.0}],"mesh":[{"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":"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":"D010582","descriptor_name":"Bacteriophage lambda","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010582","descriptor_name":"Bacteriophage lambda","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010582","descriptor_name":"Bacteriophage lambda","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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:10.1021/acs.jcim.9b00685","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00685","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:31580657","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31580657","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 chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.800000011920929,"id":"https://metadata.un.org/sdg/6","display_name":"Clean water and sanitation"}],"awards":[{"id":"https://openalex.org/G1908605997","display_name":null,"funder_award_id":"23/12/2012(ii)EU-V","funder_id":"https://openalex.org/F4320320767","funder_display_name":"University Grants Commission"}],"funders":[{"id":"https://openalex.org/F4320320767","display_name":"University Grants Commission","ror":"https://ror.org/04p800546"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W1585692887","https://openalex.org/W1604437810","https://openalex.org/W1967737979","https://openalex.org/W1968185864","https://openalex.org/W1971811725","https://openalex.org/W1973870738","https://openalex.org/W1976499671","https://openalex.org/W1978245406","https://openalex.org/W1988368932","https://openalex.org/W1989223816","https://openalex.org/W1989430838","https://openalex.org/W1992210744","https://openalex.org/W1992810339","https://openalex.org/W2006205176","https://openalex.org/W2013160922","https://openalex.org/W2016097548","https://openalex.org/W2016487696","https://openalex.org/W2023348541","https://openalex.org/W2024905541","https://openalex.org/W2025363776","https://openalex.org/W2026598193","https://openalex.org/W2027087381","https://openalex.org/W2027408247","https://openalex.org/W2032205265","https://openalex.org/W2035737796","https://openalex.org/W2036318240","https://openalex.org/W2044841023","https://openalex.org/W2049878642","https://openalex.org/W2067174909","https://openalex.org/W2070550775","https://openalex.org/W2070676606","https://openalex.org/W2086270305","https://openalex.org/W2086887083","https://openalex.org/W2089608829","https://openalex.org/W2090393756","https://openalex.org/W2093814864","https://openalex.org/W2094493821","https://openalex.org/W2096441380","https://openalex.org/W2106140689","https://openalex.org/W2113495126","https://openalex.org/W2117152823","https://openalex.org/W2123491649","https://openalex.org/W2128560189","https://openalex.org/W2138825634","https://openalex.org/W2144062946","https://openalex.org/W2148903697","https://openalex.org/W2150981663","https://openalex.org/W2160822610","https://openalex.org/W2167404361","https://openalex.org/W2222563105","https://openalex.org/W2320675468","https://openalex.org/W2321285973","https://openalex.org/W2602360663","https://openalex.org/W2769325957","https://openalex.org/W2951392003"],"related_works":["https://openalex.org/W2049158685","https://openalex.org/W2076108054","https://openalex.org/W2062280983","https://openalex.org/W2010816189","https://openalex.org/W2029798964","https://openalex.org/W2030814217","https://openalex.org/W2092208672","https://openalex.org/W2023309215","https://openalex.org/W1603616915","https://openalex.org/W4281654480"],"abstract_inverted_index":{"Noncovalent":[0],"interactions":[1],"between":[2],"protein":[3,22,69,82,164],"and":[4,27,83,92,96,165,200],"DNA":[5,26,85,166],"are":[6,88,148,169,185],"important":[7,17],"to":[8,159,187,192],"comprehend":[9],"different":[10],"biological":[11],"activities":[12],"in":[13,90,105,170,172],"living":[14],"organisms.":[15],"One":[16],"issue":[18],"is":[19,125],"how":[20],"the":[21,24,28,31,36,53,58,62,67,78,81,84,93,122,141,144,163,173,194],"identifies":[23],"target":[25],"influence":[29],"of":[30,52,61,66,77,80,98,112,130,138,196],"resulting":[32],"protein-DNA":[33,54,198],"complex":[34,55,199],"on":[35],"hydration":[37],"environment":[38],"around":[39,100,162],"it.":[40],"In":[41],"this":[42],"study,":[43],"we":[44],"have":[45,102],"carried":[46],"out":[47],"atomistic":[48],"molecular":[49],"dynamics":[50],"simulations":[51],"formed":[56],"by":[57],"dimeric":[59],"form":[60],"\u03b1-helical":[63],"N-terminal":[64],"domain":[65],"\u03bb-repressor":[68],"with":[70,150],"its":[71,202],"operator":[72],"DNA.":[73],"Local":[74],"heterogeneous":[75],"flexibilities":[76],"residues":[79,167],"components":[86],"that":[87,127,168,178],"involved":[89],"binding":[91],"microscopic":[94],"structure":[95],"ordering":[97,139],"water":[99,119,133,152,183],"those":[101],"been":[103,157],"investigated":[104],"detail.":[106],"The":[107,154],"calculations":[108],"revealed":[109],"concurrent":[110],"existence":[111],"highly":[113,180],"ordered":[114,181],"as":[115,117,189],"well":[116],"disordered":[118],"molecules":[120,134,184],"at":[121,140],"interface.":[123],"It":[124],"found":[126,158],"a":[128,197],"fraction":[129],"doubly":[131],"coordinated":[132,149],"exhibit":[135],"high":[136],"degree":[137],"interface,":[142],"while":[143],"randomly":[145],"oriented":[146],"ones":[147],"three":[151],"molecules.":[153],"effect":[155],"has":[156],"be":[160],"more":[161],"contact":[171],"complexed":[174],"state.":[175],"We":[176],"believe":[177],"such":[179],"two-coordinated":[182],"likely":[186],"act":[188],"an":[190],"adhesive":[191],"facilitate":[193],"formation":[195],"maintain":[201],"structural":[203],"stability.":[204]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-27T08:28:00.272161","created_date":"2025-10-10T00:00:00"}