{"id":"https://openalex.org/W2061762615","doi":"https://doi.org/10.3390/e17031477","title":"Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins","display_name":"Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins","publication_year":2015,"publication_date":"2015-03-23","ids":{"openalex":"https://openalex.org/W2061762615","doi":"https://doi.org/10.3390/e17031477","mag":"2061762615"},"language":"en","primary_location":{"id":"doi:10.3390/e17031477","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e17031477","pdf_url":"https://www.mdpi.com/1099-4300/17/3/1477/pdf?version=1427106116","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1099-4300/17/3/1477/pdf?version=1427106116","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007069015","display_name":"Barbara Kalinowska","orcid":null},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Barbara Kalinowska","raw_affiliation_strings":["Department of Bioinformatics and Telemedicine, Collegium Medium, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland","Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-348 \u0141ojasiewicza 11, Krakow, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Telemedicine, Collegium Medium, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland","institution_ids":["https://openalex.org/I126596746"]},{"raw_affiliation_string":"Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-348 \u0141ojasiewicza 11, Krakow, Poland","institution_ids":["https://openalex.org/I126596746"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068559370","display_name":"Mateusz Banach","orcid":"https://orcid.org/0000-0003-1806-9877"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Mateusz Banach","raw_affiliation_strings":["Department of Bioinformatics and Telemedicine, Collegium Medium, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland","Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-348 \u0141ojasiewicza 11, Krakow, Poland"],"raw_orcid":"https://orcid.org/0000-0003-1806-9877","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Telemedicine, Collegium Medium, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland","institution_ids":["https://openalex.org/I126596746"]},{"raw_affiliation_string":"Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-348 \u0141ojasiewicza 11, Krakow, Poland","institution_ids":["https://openalex.org/I126596746"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027144155","display_name":"Leszek Konieczny","orcid":null},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Leszek Konieczny","raw_affiliation_strings":["Chair of Medical Biochemistry, Collegium Medicum, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chair of Medical Biochemistry, Collegium Medicum, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland","institution_ids":["https://openalex.org/I126596746"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087239926","display_name":"Irena Roterman","orcid":"https://orcid.org/0000-0003-3652-9099"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Irena Roterman","raw_affiliation_strings":["Department of Bioinformatics and Telemedicine, Collegium Medium, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Telemedicine, Collegium Medium, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland","institution_ids":["https://openalex.org/I126596746"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5087239926"],"corresponding_institution_ids":["https://openalex.org/I126596746"],"apc_list":{"value":2000,"currency":"CHF","value_usd":2165},"apc_paid":{"value":2000,"currency":"CHF","value_usd":2165},"fwci":3.916,"has_fulltext":true,"cited_by_count":70,"citation_normalized_percentile":{"value":0.94218971,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"17","issue":"3","first_page":"1477","last_page":"1507"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and 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/T10044","display_name":"Protein Structure and 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":0.9972000122070312,"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/T10604","display_name":"RNA Research and Splicing","score":0.9926000237464905,"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/entropy","display_name":"Entropy (arrow of time)","score":0.510882556438446},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5098325610160828},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.504055380821228},{"id":"https://openalex.org/keywords/core-protein","display_name":"Core protein","score":0.43094420433044434},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.40770506858825684},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39846107363700867},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3939174711704254},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.37494492530822754},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.32316961884498596},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.29546353220939636},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.2634665071964264},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2470497488975525},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.24105018377304077}],"concepts":[{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.510882556438446},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5098325610160828},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.504055380821228},{"id":"https://openalex.org/C2992769111","wikidata":"https://www.wikidata.org/wiki/Q830465","display_name":"Core protein","level":2,"score":0.43094420433044434},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.40770506858825684},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39846107363700867},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3939174711704254},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.37494492530822754},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.32316961884498596},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.29546353220939636},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.2634665071964264},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2470497488975525},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.24105018377304077}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3390/e17031477","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e17031477","pdf_url":"https://www.mdpi.com/1099-4300/17/3/1477/pdf?version=1427106116","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},{"id":"pmh:oai:ruj.uj.edu.pl:item/13252","is_oa":true,"landing_page_url":"http://ruj.uj.edu.pl/xmlui/handle/item/13252","pdf_url":null,"source":{"id":"https://openalex.org/S4306401249","display_name":"Jagiellonian University Repository (Jagiellonian University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I126596746","host_organization_name":"Jagiellonian University","host_organization_lineage":["https://openalex.org/I126596746"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:5d245482d3cf4b93ad1d06f5b0c5211b","is_oa":true,"landing_page_url":"https://doaj.org/article/5d245482d3cf4b93ad1d06f5b0c5211b","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Entropy, Vol 17, Iss 3, Pp 1477-1507 (2015)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/1099-4300/17/3/1477/","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3390/e17031477","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Entropy","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/e17031477","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e17031477","pdf_url":"https://www.mdpi.com/1099-4300/17/3/1477/pdf?version=1427106116","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3102339463","display_name":null,"funder_award_id":"K/ZDS/001531","funder_id":"https://openalex.org/F4320310970","funder_display_name":"Uniwersytet Jagiello\u0144ski Collegium Medicum"}],"funders":[{"id":"https://openalex.org/F4320310970","display_name":"Uniwersytet Jagiello\u0144ski Collegium Medicum","ror":"https://ror.org/03bqmcz70"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2061762615.pdf","grobid_xml":"https://content.openalex.org/works/W2061762615.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W157808733","https://openalex.org/W175377976","https://openalex.org/W181559501","https://openalex.org/W216878207","https://openalex.org/W1032438816","https://openalex.org/W1882642804","https://openalex.org/W1963789736","https://openalex.org/W1964731295","https://openalex.org/W1964976079","https://openalex.org/W1965435178","https://openalex.org/W1965555277","https://openalex.org/W1975304761","https://openalex.org/W1975798725","https://openalex.org/W1979404891","https://openalex.org/W1979764309","https://openalex.org/W1993944404","https://openalex.org/W1994367552","https://openalex.org/W1995652309","https://openalex.org/W1997870466","https://openalex.org/W2001014276","https://openalex.org/W2001840083","https://openalex.org/W2002248105","https://openalex.org/W2007400675","https://openalex.org/W2012072946","https://openalex.org/W2014050554","https://openalex.org/W2016785081","https://openalex.org/W2017422947","https://openalex.org/W2018367009","https://openalex.org/W2022496255","https://openalex.org/W2023400093","https://openalex.org/W2026593599","https://openalex.org/W2027870104","https://openalex.org/W2034671873","https://openalex.org/W2048694221","https://openalex.org/W2049017264","https://openalex.org/W2049033408","https://openalex.org/W2053418558","https://openalex.org/W2079898330","https://openalex.org/W2080896401","https://openalex.org/W2085939254","https://openalex.org/W2086808970","https://openalex.org/W2088844185","https://openalex.org/W2091559870","https://openalex.org/W2092424728","https://openalex.org/W2098481391","https://openalex.org/W2105387956","https://openalex.org/W2106034800","https://openalex.org/W2108067237","https://openalex.org/W2108502557","https://openalex.org/W2114441129","https://openalex.org/W2132720084","https://openalex.org/W2146256775","https://openalex.org/W2152282874","https://openalex.org/W2156954132","https://openalex.org/W2413132705","https://openalex.org/W4233439880"],"related_works":["https://openalex.org/W2362793208","https://openalex.org/W2077170224","https://openalex.org/W1946758633","https://openalex.org/W1985606919","https://openalex.org/W1973430331","https://openalex.org/W2792050031","https://openalex.org/W2040554061","https://openalex.org/W1976939267","https://openalex.org/W2015266956","https://openalex.org/W2051647984"],"abstract_inverted_index":{"The":[0],"fuzzy":[1,61],"oil":[2,62],"drop":[3,63],"model,":[4,64,113],"a":[5],"tool":[6],"which":[7,81,92],"can":[8],"be":[9],"used":[10],"to":[11,30,45,67,119],"study":[12],"the":[13,16,25,31,40,57,60,72,79,87,101,107,110,132],"structure":[14,88],"of":[15,27,42,59,74,89,109,134],"hydrophobic":[17,111,139],"core":[18,112],"in":[19,24,56,95,136],"proteins,":[20],"has":[21],"been":[22],"applied":[23],"analysis":[26],"proteins":[28,97],"belonging":[29],"jumonji":[32,96],"group\u2014JARID2,":[33],"JARID1A,":[34],"JARID1B":[35],"and":[36,51],"JARID1D\u2014proteins":[37],"that":[38,115],"share":[39],"property":[41],"being":[43],"able":[44],"interact":[46],"with":[47],"DNA.":[48],"Their":[49],"ARID":[50],"PHD":[52],"domains,":[53],"when":[54],"analyzed":[55],"context":[58],"are":[65,93],"found":[66],"exhibit":[68],"structural":[69,121],"variability":[70],"regarding":[71],"status":[73],"their":[75,83],"secondary":[76],"folds,":[77],"including":[78],"\u03b2-hairpin":[80],"determines":[82],"biological":[84],"function.":[85],"Additionally,":[86],"disordered":[90],"fragments":[91,117],"present":[94],"(as":[98],"confirmed":[99],"by":[100,127],"DisProt":[102],"database)":[103],"is":[104,125],"explained":[105],"on":[106],"grounds":[108],"suggesting":[114],"such":[116],"contribute":[118],"tertiary":[120],"stabilization.":[122],"This":[123],"conclusion":[124],"supported":[126],"divergence":[128],"entropy":[129],"measurements,":[130],"expressing":[131],"degree":[133],"ordering":[135],"each":[137],"protein\u2019s":[138],"core.":[140]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":2}],"updated_date":"2026-06-14T07:44:22.658603","created_date":"2025-10-10T00:00:00"}