{"id":"https://openalex.org/W4391760740","doi":"https://doi.org/10.1093/bioinformatics/btae076","title":"Dynamic correlations: exact and approximate methods for mutual information","display_name":"Dynamic correlations: exact and approximate methods for mutual information","publication_year":2024,"publication_date":"2024-02-01","ids":{"openalex":"https://openalex.org/W4391760740","doi":"https://doi.org/10.1093/bioinformatics/btae076","pmid":"https://pubmed.ncbi.nlm.nih.gov/38341647"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae076","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae076","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae076/56659528/btae076.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae076/56659528/btae076.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114909932","display_name":"Kemal Demirta\u015f","orcid":"https://orcid.org/0009-0000-1420-1813"},"institutions":[{"id":"https://openalex.org/I4405392","display_name":"Bo\u011fazi\u00e7i University","ror":"https://ror.org/03z9tma90","country_code":"TR","type":"education","lineage":["https://openalex.org/I4405392"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Kemal Demirta\u015f","raw_affiliation_strings":["Department of Chemical Engineering, Bogazici University , 34342 Istanbul, Turkey","Polymer Research Center, Bogazici University , 34342 Istanbul, Turkey","Department of Chemical Engineering, Bogazici University, Istanbul, 34342, Turkey","Polymer Research Center, Bogazici University, Istanbul, 34342, Turkey"],"raw_orcid":"https://orcid.org/0009-0000-1420-1813","affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Bogazici University , 34342 Istanbul, Turkey","institution_ids":["https://openalex.org/I4405392"]},{"raw_affiliation_string":"Polymer Research Center, Bogazici University , 34342 Istanbul, Turkey","institution_ids":["https://openalex.org/I4405392"]},{"raw_affiliation_string":"Department of Chemical Engineering, Bogazici University, Istanbul, 34342, Turkey","institution_ids":["https://openalex.org/I4405392"]},{"raw_affiliation_string":"Polymer Research Center, Bogazici University, Istanbul, 34342, Turkey","institution_ids":["https://openalex.org/I4405392"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038786006","display_name":"Burak Erman","orcid":"https://orcid.org/0000-0002-2496-6059"},"institutions":[{"id":"https://openalex.org/I1351752","display_name":"Ko\u00e7 University","ror":"https://ror.org/00jzwgz36","country_code":"TR","type":"education","lineage":["https://openalex.org/I1351752"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Burak Erman","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Koc University , 34450 Istanbul, Turkey","Department of Chemical and Biological Engineering, Koc University, Istanbul, 34450, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-2496-6059","affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Koc University , 34450 Istanbul, Turkey","institution_ids":["https://openalex.org/I1351752"]},{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Koc University, Istanbul, 34450, Turkey","institution_ids":["https://openalex.org/I1351752"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038256975","display_name":"T\u00fcrkan Halilo\u01e7lu","orcid":"https://orcid.org/0000-0002-1279-5803"},"institutions":[{"id":"https://openalex.org/I4405392","display_name":"Bo\u011fazi\u00e7i University","ror":"https://ror.org/03z9tma90","country_code":"TR","type":"education","lineage":["https://openalex.org/I4405392"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"T\u00fcrkan Halilo\u011flu","raw_affiliation_strings":["Department of Chemical Engineering, Bogazici University , 34342 Istanbul, Turkey","Polymer Research Center, Bogazici University , 34342 Istanbul, Turkey","Polymer Research Center, Bogazici University, Istanbul, 34342, Turkey","Department of Chemical Engineering, Bogazici University, Istanbul, 34342, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-1279-5803","affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Bogazici University , 34342 Istanbul, Turkey","institution_ids":["https://openalex.org/I4405392"]},{"raw_affiliation_string":"Polymer Research Center, Bogazici University , 34342 Istanbul, Turkey","institution_ids":["https://openalex.org/I4405392"]},{"raw_affiliation_string":"Polymer Research Center, Bogazici University, Istanbul, 34342, Turkey","institution_ids":["https://openalex.org/I4405392"]},{"raw_affiliation_string":"Department of Chemical Engineering, Bogazici University, Istanbul, 34342, Turkey","institution_ids":["https://openalex.org/I4405392"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5038256975","https://openalex.org/A5038786006"],"corresponding_institution_ids":["https://openalex.org/I1351752","https://openalex.org/I4405392"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.6105,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.93470747,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"40","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.91839998960495,"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":0.91839998960495,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0333000011742115,"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":0.013000000268220901,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6513674259185791},{"id":"https://openalex.org/keywords/mutual-information","display_name":"Mutual information","score":0.5042263269424438},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3507377505302429},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32620707154273987},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2427803874015808}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6513674259185791},{"id":"https://openalex.org/C152139883","wikidata":"https://www.wikidata.org/wiki/Q252973","display_name":"Mutual information","level":2,"score":0.5042263269424438},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3507377505302429},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32620707154273987},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2427803874015808}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014452","descriptor_name":"Ubiquitins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014452","descriptor_name":"Ubiquitins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014452","descriptor_name":"Ubiquitins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014452","descriptor_name":"Ubiquitins","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":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae076","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae076","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae076/56659528/btae076.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38341647","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38341647","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:pubmedcentral.nih.gov:10898342","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10898342","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10898342/pdf/btae076.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae076","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae076","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae076/56659528/btae076.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2229154063","display_name":"Proteinlerde Nadir Ara Yap\u0131lar ve Konformasyonel Ge\u00e7i\u015f Yollar\u0131: \u0130\u015flevsel Mekanizma ve Kinetik Davran\u0131\u015f\u0131 Tahmin Eden Hibrit Hesapsal Yakla\u015f\u0131mlar","funder_award_id":"119F392","funder_id":"https://openalex.org/F4320322626","funder_display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu"}],"funders":[{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4391760740.pdf"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1527591909","https://openalex.org/W1890755677","https://openalex.org/W1965885513","https://openalex.org/W1978607920","https://openalex.org/W1991669238","https://openalex.org/W2004577830","https://openalex.org/W2008545402","https://openalex.org/W2009018090","https://openalex.org/W2009123297","https://openalex.org/W2030124895","https://openalex.org/W2043224156","https://openalex.org/W2049598343","https://openalex.org/W2092006899","https://openalex.org/W2123182960","https://openalex.org/W2218712061","https://openalex.org/W2294044832","https://openalex.org/W2335891899","https://openalex.org/W2360781516","https://openalex.org/W2480986332","https://openalex.org/W2591912476","https://openalex.org/W2620265724","https://openalex.org/W2754724354","https://openalex.org/W2767331364","https://openalex.org/W2889334945","https://openalex.org/W2901969285","https://openalex.org/W3035324832","https://openalex.org/W3046218096","https://openalex.org/W3080855264","https://openalex.org/W3084762951","https://openalex.org/W3100807572","https://openalex.org/W3104746727","https://openalex.org/W3128141025","https://openalex.org/W3173432813","https://openalex.org/W3182702903","https://openalex.org/W3184269784","https://openalex.org/W3185257695","https://openalex.org/W4282935889","https://openalex.org/W4295757322","https://openalex.org/W4296026702"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2466816617","https://openalex.org/W2073681303","https://openalex.org/W1970834875","https://openalex.org/W842936808","https://openalex.org/W3174028392","https://openalex.org/W2390279801"],"abstract_inverted_index":{"MOTIVATION:":[0],"Proteins":[1],"are":[2,108,258],"dynamic":[3,40,214],"entities":[4],"that":[5],"undergo":[6],"conformational":[7],"changes":[8],"critical":[9],"for":[10,24,89,101,106,124,129,150,155,208],"their":[11,29],"functions.":[12],"Understanding":[13],"the":[14,51,59,72,85,115,132,137,158,167,175,204,218,222,246],"communication":[15],"pathways":[16],"and":[17,46,53,62,71,103,126,152],"information":[18,35,93,144,190,256],"transfer":[19],"within":[20,221],"proteins":[21],"is":[22,162],"crucial":[23],"elucidating":[25],"allosteric":[26,79],"interactions":[27],"in":[28,77,165,174],"mechanisms.":[30],"This":[31],"study":[32],"utilizes":[33],"mutual":[34,92,143],"(MI)":[36],"analysis":[37],"to":[38,244],"probe":[39],"allostery.":[41],"Using":[42],"two":[43],"cases,":[44],"Ubiquitin":[45,102,125,151],"PLpro,":[47,178],"we":[48],"have":[49],"evaluated":[50],"accuracy":[52],"limitations":[54],"of":[55,120,134,147,170,177,188,212,248],"different":[56],"approximations":[57,187,211],"including":[58],"exact":[60],"anisotropic":[61,168],"isotropic":[63,68,159],"models,":[64],"multivariate":[65,138],"Gaussian":[66,69,73,139,160,210],"model,":[67,70],"Network":[74],"Model":[75],"(GNM)":[76],"revealing":[78],"interactions.":[80],"RESULTS:":[81],"Our":[82],"findings":[83],"emphasize":[84],"required":[86],"trajectory":[87,206],"length":[88],"capturing":[90],"accurate":[91],"profiles.":[94],"Long":[95],"molecular":[96],"dynamics":[97,220,229],"trajectories,":[98],"1":[99,127],"ms":[100],"100":[104],"\u00b5s":[105,123,128],"PLpro":[107,130],"used":[109,237],"as":[110,192,239],"benchmarks,":[111],"assuming":[112],"they":[113],"represent":[114],"ground":[116],"truth.":[117],"Trajectory":[118],"lengths":[119,207],"approximately":[121],"5":[122,148],"marked":[131],"onset":[133],"convergence,":[135],"while":[136],"model":[140,161,196],"accurately":[141],"captured":[142],"with":[145],"trajectories":[146],"ns":[149,154],"350":[153],"PLpro.":[156],"However,":[157],"less":[163],"successful":[164],"representing":[166],"nature":[169],"protein":[171],"dynamics,":[172],"particularly":[173],"case":[176],"highlighting":[179],"its":[180],"limitations.":[181],"The":[182,225],"GNM,":[183,226],"however,":[184],"provides":[185],"reasonable":[186],"long-range":[189],"exchange":[191],"a":[193,199,240],"minimalist":[194],"network":[195],"based":[197],"on":[198,217],"single":[200],"crystal":[201],"structure.":[202],"Overall,":[203],"optimum":[205],"effective":[209],"long-time":[213],"behavior":[215],"depend":[216],"inherent":[219],"protein's":[223],"topology.":[224],"by":[227],"showcasing":[228],"across":[230],"relatively":[231],"diverse":[232],"time":[233],"scales,":[234],"can":[235],"be":[236],"either":[238],"standalone":[241],"method":[242],"or":[243],"gauge":[245],"adequacy":[247],"MD":[249],"simulation":[250],"lengths.":[251],"AVAILABILITY":[252],"AND":[253],"IMPLEMENTATION:":[254],"Mutual":[255],"codes":[257],"available":[259],"at":[260],"https://github.com/kemaldemirtas/prc-MI.git.":[261]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":3}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}
