{"id":"https://openalex.org/W2052166746","doi":"https://doi.org/10.1371/journal.pcbi.1000170","title":"Insights into Protein\u2013DNA Interactions through Structure Network Analysis","display_name":"Insights into Protein\u2013DNA Interactions through Structure Network Analysis","publication_year":2008,"publication_date":"2008-09-04","ids":{"openalex":"https://openalex.org/W2052166746","doi":"https://doi.org/10.1371/journal.pcbi.1000170","mag":"2052166746","pmid":"https://pubmed.ncbi.nlm.nih.gov/18773096"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000170","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000170","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000170&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000170&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032845716","display_name":"R. Sathyapriya","orcid":"https://orcid.org/0000-0002-7379-3086"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"R. Sathyapriya","raw_affiliation_strings":["Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India","Molecular Biophysics Unit, Indian Institute of Science Bangalore India"],"affiliations":[{"raw_affiliation_string":"Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India","institution_ids":["https://openalex.org/I59270414"]},{"raw_affiliation_string":"Molecular Biophysics Unit, Indian Institute of Science Bangalore India","institution_ids":["https://openalex.org/I59270414"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016171735","display_name":"M. S. Vijayabaskar","orcid":"https://orcid.org/0000-0002-5559-9394"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"M. S. Vijayabaskar","raw_affiliation_strings":["Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India","Molecular Biophysics Unit, Indian Institute of Science Bangalore India"],"affiliations":[{"raw_affiliation_string":"Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India","institution_ids":["https://openalex.org/I59270414"]},{"raw_affiliation_string":"Molecular Biophysics Unit, Indian Institute of Science Bangalore India","institution_ids":["https://openalex.org/I59270414"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031607667","display_name":"Saraswathi Vishveshwara","orcid":"https://orcid.org/0000-0002-5035-7433"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Saraswathi Vishveshwara","raw_affiliation_strings":["Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India","Molecular Biophysics Unit, Indian Institute of Science Bangalore India"],"affiliations":[{"raw_affiliation_string":"Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India","institution_ids":["https://openalex.org/I59270414"]},{"raw_affiliation_string":"Molecular Biophysics Unit, Indian Institute of Science Bangalore India","institution_ids":["https://openalex.org/I59270414"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5031607667"],"corresponding_institution_ids":["https://openalex.org/I59270414"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.9364,"has_fulltext":true,"cited_by_count":80,"citation_normalized_percentile":{"value":0.85384583,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"4","issue":"9","first_page":"e1000170","last_page":"e1000170"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9955999851226807,"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/computational-biology","display_name":"Computational biology","score":0.5911808013916016},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.5094147324562073},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5086989998817444},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.4493447244167328},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.44216388463974},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.42591744661331177},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4215613603591919},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3861766457557678},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29975295066833496},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.20528173446655273},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17019259929656982},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1353505253791809}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5911808013916016},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5094147324562073},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5086989998817444},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.4493447244167328},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.44216388463974},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.42591744661331177},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4215613603591919},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3861766457557678},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29975295066833496},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.20528173446655273},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17019259929656982},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1353505253791809}],"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":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","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":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1000170","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000170","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000170&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:18773096","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18773096","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.274.6023","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.274.6023","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/8a/68/PLoS_Comput_Biol_2008_Sep_5_4(9)_e1000170.tar.gz","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:cbf17e5a9d4f489f877a95845c45675e","is_oa":true,"landing_page_url":"https://doaj.org/article/cbf17e5a9d4f489f877a95845c45675e","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 4, Iss 9, p e1000170 (2008)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/149757","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Insights_into_Protein_DNA_Interactions_through_Structure_Network_Analysis/149757","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:2518215","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2518215","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000170","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000170","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000170&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2052166746.pdf","grobid_xml":"https://content.openalex.org/works/W2052166746.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W117652395","https://openalex.org/W301824129","https://openalex.org/W1536428180","https://openalex.org/W1943277194","https://openalex.org/W1963915837","https://openalex.org/W1971842995","https://openalex.org/W1973437120","https://openalex.org/W1974464359","https://openalex.org/W1974846059","https://openalex.org/W1981482769","https://openalex.org/W1983703472","https://openalex.org/W1985956244","https://openalex.org/W1987958688","https://openalex.org/W2004263936","https://openalex.org/W2009158394","https://openalex.org/W2036259941","https://openalex.org/W2037099334","https://openalex.org/W2039478144","https://openalex.org/W2040007286","https://openalex.org/W2042303986","https://openalex.org/W2042454335","https://openalex.org/W2062926294","https://openalex.org/W2066578663","https://openalex.org/W2070871842","https://openalex.org/W2075855826","https://openalex.org/W2086315977","https://openalex.org/W2088311925","https://openalex.org/W2091977789","https://openalex.org/W2101414808","https://openalex.org/W2130479394","https://openalex.org/W2137154596","https://openalex.org/W2144792857","https://openalex.org/W2145382385","https://openalex.org/W2154447604","https://openalex.org/W2154465624","https://openalex.org/W2157047993","https://openalex.org/W2159291387","https://openalex.org/W2165608108","https://openalex.org/W2166248605","https://openalex.org/W2215513048","https://openalex.org/W3145128584","https://openalex.org/W4246607059","https://openalex.org/W4285719527","https://openalex.org/W6610829035"],"related_works":["https://openalex.org/W4229728790","https://openalex.org/W2800059693","https://openalex.org/W2066232588","https://openalex.org/W4377086792","https://openalex.org/W2099913238","https://openalex.org/W2767490506","https://openalex.org/W1987705964","https://openalex.org/W2914490533","https://openalex.org/W4226462951","https://openalex.org/W1841073402"],"abstract_inverted_index":{"Protein-DNA":[0],"interactions":[1,26],"are":[2],"crucial":[3],"for":[4,144,216],"many":[5],"cellular":[6],"processes.":[7],"Now":[8],"with":[9,122,240],"the":[10,22,34,42,46,78,86,93,101,104,111,114,123,136,145,152,155,168,176,190,196,223,226,237,241,253,262,265,274,277],"increased":[11],"availability":[12],"of":[13,15,24,71,77,89,107,110,116,125,135,151,157,162,164,170,181,189,219,225,235,244,264,279],"structures":[14],"protein-DNA":[16,25,66,120,177,220,227,266],"complexes,":[17],"gaining":[18],"deeper":[19,259],"insights":[20],"into":[21,261],"nature":[23,275],"has":[27,140],"become":[28],"possible.":[29],"Earlier,":[30],"investigations":[31,80],"have":[32,81,201],"characterized":[33],"interface":[35,191,228],"properties":[36],"by":[37,63,204,269],"considering":[38,64],"pairwise":[39,51,206],"interactions.":[40,281],"However,":[41],"information":[43],"communicated":[44],"along":[45,175],"interfaces":[47],"is":[48],"rarely":[49],"a":[50,57,65,69,132,212,217,232,258],"phenomenon,":[52],"and":[53,92,103,139,167,195,276],"we":[54,210,250],"feel":[55],"that":[56,252],"global":[58],"picture":[59],"can":[60],"be":[61],"obtained":[62],"complex":[67],"as":[68],"network":[70,95,129],"noncovalently":[72],"interacting":[73,137,165],"systems.":[74],"Furthermore,":[75],"most":[76],"earlier":[79],"been":[82,141,202],"carried":[83],"out":[84],"from":[85],"protein":[87],"point":[88],"view":[90,134],"(protein-centric),":[91],"present":[94,254],"approach":[96],"aims":[97],"to":[98,118],"combine":[99],"both":[100],"protein-centric":[102],"DNA-centric":[105],"points":[106],"view.":[108],"Part":[109],"study":[112,153],"involves":[113,154],"development":[115,124],"methodology":[117],"investigate":[119],"graphs/networks":[121],"key":[126],"parameters.":[127],"A":[128,179],"representation":[130],"provides":[131,231,257],"holistic":[133],"surface":[138],"reported":[142],"here":[143],"first":[146],"time.":[147],"The":[148],"second":[149],"part":[150],"analyses":[156],"these":[158,280],"graphs":[159],"in":[160,185,193,246],"terms":[161],"clusters":[163,184,192],"residues":[166,173],"identification":[169],"highly":[171],"connected":[172],"(hubs)":[174],"interface.":[178],"predominance":[180],"deoxyribose-amino":[182],"acid":[183],"beta-sheet":[186],"proteins,":[187],"distinction":[188],"helix-turn-helix,":[194],"zipper-type":[197],"proteins":[198,238],"would":[199],"not":[200],"possible":[203],"conventional":[205],"interaction":[207],"analysis.":[208],"Additionally,":[209],"propose":[211],"potential":[213],"classification":[214],"scheme":[215],"set":[218],"complexes":[221],"on":[222,273],"basis":[224],"clusters.":[229],"This":[230],"general":[233],"idea":[234],"how":[236],"interact":[239],"different":[242,247],"components":[243],"DNA":[245],"complexes.":[248],"Thus,":[249],"believe":[251],"graph-based":[255],"method":[256],"insight":[260],"analysis":[263],"recognition":[267],"mechanisms":[268],"throwing":[270],"more":[271],"light":[272],"specificity":[278]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":10}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}