{"id":"https://openalex.org/W4409318776","doi":"https://doi.org/10.1186/s13321-025-00997-3","title":"Unveiling polyphenol-protein interactions: a comprehensive computational analysis","display_name":"Unveiling polyphenol-protein interactions: a comprehensive computational analysis","publication_year":2025,"publication_date":"2025-04-10","ids":{"openalex":"https://openalex.org/W4409318776","doi":"https://doi.org/10.1186/s13321-025-00997-3","pmid":"https://pubmed.ncbi.nlm.nih.gov/40211304"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-00997-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00997-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00997-3","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00997-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032088268","display_name":"Samo Le\u0161nik","orcid":"https://orcid.org/0000-0002-0613-6959"},"institutions":[{"id":"https://openalex.org/I37696226","display_name":"University of Maribor","ror":"https://ror.org/01d5jce07","country_code":"SI","type":"education","lineage":["https://openalex.org/I37696226"]},{"id":"https://openalex.org/I4210112522","display_name":"Institute for Environmental Protection and Sensors","ror":"https://ror.org/01sh25n93","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210112522"]}],"countries":["SI"],"is_corresponding":true,"raw_author_name":"Samo Le\u0161nik","raw_affiliation_strings":["IOS, Institute of Environmental Protection and Sensors, Beloruska 7, 2000, Maribor, Slovenia","Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, 2000, Maribor, Slovenia"],"affiliations":[{"raw_affiliation_string":"IOS, Institute of Environmental Protection and Sensors, Beloruska 7, 2000, Maribor, Slovenia","institution_ids":["https://openalex.org/I4210112522"]},{"raw_affiliation_string":"Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, 2000, Maribor, Slovenia","institution_ids":["https://openalex.org/I37696226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062349630","display_name":"Marko Juki\u010d","orcid":"https://orcid.org/0000-0001-6083-5024"},"institutions":[{"id":"https://openalex.org/I118905719","display_name":"University of Primorska","ror":"https://ror.org/05xefg082","country_code":"SI","type":"education","lineage":["https://openalex.org/I118905719"]},{"id":"https://openalex.org/I37696226","display_name":"University of Maribor","ror":"https://ror.org/01d5jce07","country_code":"SI","type":"education","lineage":["https://openalex.org/I37696226"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Marko Juki\u0107","raw_affiliation_strings":["Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, 6000, Koper, Slovenia","Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, 2000, Maribor, Slovenia"],"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, 6000, Koper, Slovenia","institution_ids":["https://openalex.org/I118905719"]},{"raw_affiliation_string":"Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, 2000, Maribor, Slovenia","institution_ids":["https://openalex.org/I37696226"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003060699","display_name":"Urban Bren","orcid":"https://orcid.org/0000-0002-8806-3019"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Urban Bren","raw_affiliation_strings":["Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, 6000, Koper, Slovenia. urban.bren@um.si","IOS, Institute of Environmental Protection and Sensors, Beloruska 7, 2000, Maribor, Slovenia. urban.bren@um.si","Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, 2000, Maribor, Slovenia. urban.bren@um.si"],"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, 6000, Koper, Slovenia. urban.bren@um.si","institution_ids":[]},{"raw_affiliation_string":"IOS, Institute of Environmental Protection and Sensors, Beloruska 7, 2000, Maribor, Slovenia. urban.bren@um.si","institution_ids":[]},{"raw_affiliation_string":"Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, 2000, Maribor, Slovenia. urban.bren@um.si","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5032088268"],"corresponding_institution_ids":["https://openalex.org/I37696226","https://openalex.org/I4210112522"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":7.5496,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.97564642,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"17","issue":"1","first_page":"50","last_page":"50"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.996999979019165,"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/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.996999979019165,"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":0.9950000047683716,"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/T10035","display_name":"Phytochemicals and Antioxidant Activities","score":0.9943000078201294,"subfield":{"id":"https://openalex.org/subfields/2704","display_name":"Biochemistry"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/polyphenol","display_name":"Polyphenol","score":0.7601864337921143},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6389749646186829},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5586148500442505},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.48960739374160767},{"id":"https://openalex.org/keywords/protein-dynamics","display_name":"Protein dynamics","score":0.4303722381591797},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4173051118850708},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.4142674207687378},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.36741745471954346},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28933680057525635},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.25163763761520386},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.20832815766334534}],"concepts":[{"id":"https://openalex.org/C70899900","wikidata":"https://www.wikidata.org/wiki/Q290439","display_name":"Polyphenol","level":3,"score":0.7601864337921143},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6389749646186829},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5586148500442505},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.48960739374160767},{"id":"https://openalex.org/C2775981520","wikidata":"https://www.wikidata.org/wiki/Q17156992","display_name":"Protein dynamics","level":3,"score":0.4303722381591797},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4173051118850708},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.4142674207687378},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.36741745471954346},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28933680057525635},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.25163763761520386},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.20832815766334534},{"id":"https://openalex.org/C2778004101","wikidata":"https://www.wikidata.org/wiki/Q133948","display_name":"Antioxidant","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-00997-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00997-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00997-3","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:40211304","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40211304","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 cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:38cb93adccd344e8af9864161d70ce2c","is_oa":true,"landing_page_url":"https://doaj.org/article/38cb93adccd344e8af9864161d70ce2c","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-21 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11983793","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11983793","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-00997-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00997-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00997-3","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Clean water and sanitation","id":"https://metadata.un.org/sdg/6","score":0.7799999713897705}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322554","display_name":"Javna Agencija za Raziskovalno Dejavnost RS","ror":"https://ror.org/059bp8k51"},{"id":"https://openalex.org/F4320323641","display_name":"Vedeck\u00e1 Grantov\u00e1 Agent\u00fara M\u0160VVa\u0160 SR a SAV","ror":"https://ror.org/044gwpv05"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409318776.pdf","grobid_xml":"https://content.openalex.org/works/W4409318776.grobid-xml"},"referenced_works_count":73,"referenced_works":["https://openalex.org/W625272620","https://openalex.org/W1914622032","https://openalex.org/W1975430993","https://openalex.org/W1975948225","https://openalex.org/W1981164308","https://openalex.org/W1984358846","https://openalex.org/W1988964426","https://openalex.org/W1991960405","https://openalex.org/W1994938913","https://openalex.org/W2003356525","https://openalex.org/W2021520922","https://openalex.org/W2025816743","https://openalex.org/W2027493931","https://openalex.org/W2030469769","https://openalex.org/W2034600442","https://openalex.org/W2048866816","https://openalex.org/W2051167017","https://openalex.org/W2055075339","https://openalex.org/W2061079400","https://openalex.org/W2070753604","https://openalex.org/W2087621126","https://openalex.org/W2100190412","https://openalex.org/W2103815459","https://openalex.org/W2105772474","https://openalex.org/W2109154308","https://openalex.org/W2137417655","https://openalex.org/W2149332230","https://openalex.org/W2150981663","https://openalex.org/W2154105741","https://openalex.org/W2165836681","https://openalex.org/W2169678694","https://openalex.org/W2170711116","https://openalex.org/W2346930074","https://openalex.org/W2399092983","https://openalex.org/W2492986053","https://openalex.org/W2510475640","https://openalex.org/W2554703220","https://openalex.org/W2555870966","https://openalex.org/W2614021444","https://openalex.org/W2620998958","https://openalex.org/W2769925250","https://openalex.org/W2784075059","https://openalex.org/W2890239906","https://openalex.org/W2893702439","https://openalex.org/W2895398956","https://openalex.org/W2904249156","https://openalex.org/W2914130441","https://openalex.org/W2921236084","https://openalex.org/W2973922700","https://openalex.org/W2982106362","https://openalex.org/W2996421990","https://openalex.org/W3011996119","https://openalex.org/W3012876701","https://openalex.org/W3035190080","https://openalex.org/W3042609838","https://openalex.org/W3081420850","https://openalex.org/W3089496483","https://openalex.org/W3134120587","https://openalex.org/W3138509707","https://openalex.org/W3159177617","https://openalex.org/W3166013431","https://openalex.org/W3210328668","https://openalex.org/W4242869309","https://openalex.org/W4248954065","https://openalex.org/W4282565781","https://openalex.org/W4300817063","https://openalex.org/W4309922703","https://openalex.org/W4316468878","https://openalex.org/W4320485141","https://openalex.org/W4322490930","https://openalex.org/W4385295265","https://openalex.org/W4385688679","https://openalex.org/W4388142125"],"related_works":["https://openalex.org/W2772226369","https://openalex.org/W3126783617","https://openalex.org/W3093468851","https://openalex.org/W4280624450","https://openalex.org/W2121688928","https://openalex.org/W2732388178","https://openalex.org/W2806488847","https://openalex.org/W2185518315","https://openalex.org/W4388749535","https://openalex.org/W4389958586"],"abstract_inverted_index":{"Our":[0],"study":[1,182],"investigates":[2],"polyphenol-protein":[3,59,88,177,187,211],"interactions,":[4,161,188],"analyzing":[5],"their":[6,113,166],"structural":[7,48,125,222],"diversity":[8],"and":[9,75,102,260],"dynamic":[10,62,159,170],"behavior.":[11],"Analysis":[12],"of":[13,47,58,68,78,100,119,122,130,209,217,246,256,273],"the":[14,51,66,72,120,123,128,215,218,228,237,254,264],"entire":[15],"Protein":[16,219],"Data":[17,220],"Bank":[18,221],"reveals":[19],"diverse":[20,36],"polyphenolic":[21,37,194],"structures,":[22],"engaging":[23],"in":[24,87,96,140],"various":[25],"noncovalent":[26],"interactions":[27,83,142],"with":[28,143],"proteins.":[29,144],"Interactions":[30],"observed":[31,95],"across":[32,44],"crystal":[33,80,104],"structures":[34,105],"among":[35],"classes":[38],"reveal":[39],"similarities,":[40],"underscoring":[41,76],"consistent":[42,116],"patterns":[43,94],"a":[45,270],"spectrum":[46],"motifs.":[49],"On":[50],"other":[52],"hand,":[53],"molecular":[54,233],"dynamics":[55,117,234],"(MD)":[56],"simulations":[57,111],"complexes":[60],"unveil":[61],"binding":[63,73,93,134,151,212,229,248],"patterns,":[64],"highlighting":[65],"influx":[67],"water":[69,258],"molecules":[70,259],"into":[71,186,253],"site":[74],"limitations":[77],"static":[79],"structures.":[81],"Water-mediated":[82],"emerge":[84],"as":[85,106],"crucial":[86,277],"binding,":[89],"leading":[90],"to":[91,147,153,175],"variable":[92],"MD":[97,110],"simulations.":[98,235],"Comparison":[99],"high-":[101],"low-resolution":[103],"starting":[107],"points":[108],"for":[109,192,269,278],"demonstrates":[112],"robustness,":[114],"exhibiting":[115],"regardless":[118],"quality":[121],"initial":[124],"data.":[126],"Additionally,":[127],"impact":[129],"glycosylation":[131],"on":[132,224],"polyphenol":[133,150,247,265,274],"is":[135],"explored,":[136],"revealing":[137],"its":[138],"role":[139],"modulating":[141],"In":[145,202],"contrast":[146],"synthetic":[148],"drugs,":[149],"seems":[152],"exhibit":[154],"heightened":[155],"flexibility,":[156],"driven":[157],"by":[158],"water-mediated":[160],"which":[162],"may":[163],"also":[164],"facilitate":[165],"promiscuous":[167],"binding.":[168],"Comprehensive":[169],"studies":[171],"are,":[172],"therefore":[173],"essential":[174],"understand":[176],"recognition":[178,275],"mechanisms.":[179],"Overall,":[180],"our":[181,251],"provides":[183],"novel":[184],"insights":[185],"informing":[189],"future":[190],"research":[191],"harnessing":[193],"therapeutic":[195],"potential":[196],"through":[197,232],"rational":[198],"drug":[199,282],"design.Scientific":[200],"contribution:":[201],"this":[203],"study,":[204],"we":[205,240],"present":[206],"an":[207],"analysis":[208],"(natural)":[210],"conformations,":[213],"leveraging":[214],"entirety":[216],"data":[223],"polyphenols,":[225],"while":[226],"extending":[227],"conformation":[230],"sampling":[231],"For":[236],"first":[238],"time,":[239],"introduce":[241],"experimentally":[242],"supported":[243],"large-scale":[244],"systematization":[245],"patterns.":[249],"Moreover,":[250],"insight":[252],"significance":[255],"explicit":[257],"hydrogen-bond":[261],"bridging":[262],"rationalizes":[263],"promiscuity":[266],"paradigm,":[267],"advocating":[268],"deeper":[271],"understanding":[272],"mechanisms":[276],"informed":[279],"natural":[280],"compound-based":[281],"design.":[283]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":4}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
