{"id":"https://openalex.org/W2321816919","doi":"https://doi.org/10.1051/ro/2015041","title":"Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site","display_name":"Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site","publication_year":2015,"publication_date":"2015-10-05","ids":{"openalex":"https://openalex.org/W2321816919","doi":"https://doi.org/10.1051/ro/2015041","mag":"2321816919"},"language":"en","primary_location":{"id":"doi:10.1051/ro/2015041","is_oa":false,"landing_page_url":"https://doi.org/10.1051/ro/2015041","pdf_url":null,"source":{"id":"https://openalex.org/S20631277","display_name":"RAIRO - Operations Research","issn_l":"0399-0559","issn":["0399-0559","1290-3868","2804-7303"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319748","host_organization_name":"EDP Sciences","host_organization_lineage":["https://openalex.org/P4310319748","https://openalex.org/P4310319982"],"host_organization_lineage_names":["EDP Sciences","Science Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"RAIRO - Operations Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.numdam.org/item/10.1051/ro/2015041.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072455382","display_name":"Marta Kulik","orcid":"https://orcid.org/0000-0003-2381-7665"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Marta Kulik","raw_affiliation_strings":["Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland","Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088500200","display_name":"Joanna Trylska","orcid":"https://orcid.org/0000-0002-1464-5323"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Joanna Trylska","raw_affiliation_strings":["Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4654613"],"apc_list":{"value":0,"currency":"EUR","value_usd":0},"apc_paid":null,"fwci":0.2751,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.60444827,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"50","issue":"2","first_page":"375","last_page":"386"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9955000281333923,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9925000071525574,"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/aminoglycoside","display_name":"Aminoglycoside","score":0.8640727996826172},{"id":"https://openalex.org/keywords/paromomycin","display_name":"Paromomycin","score":0.5933009386062622},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5747857093811035},{"id":"https://openalex.org/keywords/kanamycin","display_name":"Kanamycin","score":0.5635824799537659},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.5593655109405518},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5364322066307068},{"id":"https://openalex.org/keywords/ribosomal-rna","display_name":"Ribosomal RNA","score":0.513428807258606},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.49746325612068176},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.43550950288772583},{"id":"https://openalex.org/keywords/stacking","display_name":"Stacking","score":0.4111919403076172},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.3744356632232666},{"id":"https://openalex.org/keywords/antibiotics","display_name":"Antibiotics","score":0.37290453910827637},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3476143181324005},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.32673072814941406},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.2769331932067871},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22381862998008728},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.21168851852416992},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.0666716992855072}],"concepts":[{"id":"https://openalex.org/C2777787772","wikidata":"https://www.wikidata.org/wiki/Q45355603","display_name":"Aminoglycoside","level":3,"score":0.8640727996826172},{"id":"https://openalex.org/C2776114741","wikidata":"https://www.wikidata.org/wiki/Q415625","display_name":"Paromomycin","level":4,"score":0.5933009386062622},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5747857093811035},{"id":"https://openalex.org/C2780920689","wikidata":"https://www.wikidata.org/wiki/Q27094615","display_name":"Kanamycin","level":3,"score":0.5635824799537659},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.5593655109405518},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5364322066307068},{"id":"https://openalex.org/C67905577","wikidata":"https://www.wikidata.org/wiki/Q215980","display_name":"Ribosomal RNA","level":3,"score":0.513428807258606},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.49746325612068176},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.43550950288772583},{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.4111919403076172},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3744356632232666},{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.37290453910827637},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3476143181324005},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.32673072814941406},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.2769331932067871},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22381862998008728},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.21168851852416992},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0666716992855072},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1051/ro/2015041","is_oa":false,"landing_page_url":"https://doi.org/10.1051/ro/2015041","pdf_url":null,"source":{"id":"https://openalex.org/S20631277","display_name":"RAIRO - Operations Research","issn_l":"0399-0559","issn":["0399-0559","1290-3868","2804-7303"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319748","host_organization_name":"EDP Sciences","host_organization_lineage":["https://openalex.org/P4310319748","https://openalex.org/P4310319982"],"host_organization_lineage_names":["EDP Sciences","Science Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"RAIRO - Operations Research","raw_type":"journal-article"},{"id":"pmh:oai:numdam.org:RO_2016__50_2_375_0","is_oa":true,"landing_page_url":"http://www.numdam.org/articles/10.1051/ro/2015041/","pdf_url":"https://www.numdam.org/item/10.1051/ro/2015041.pdf","source":{"id":"https://openalex.org/S4306402264","display_name":"French digital mathematics library (Numdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I70900168","host_organization_name":"Universit\u00e9 Savoie Mont Blanc","host_organization_lineage":["https://openalex.org/I70900168"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:numdam.org:RO_2016__50_2_375_0","is_oa":true,"landing_page_url":"http://www.numdam.org/articles/10.1051/ro/2015041/","pdf_url":"https://www.numdam.org/item/10.1051/ro/2015041.pdf","source":{"id":"https://openalex.org/S4306402264","display_name":"French digital mathematics library (Numdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I70900168","host_organization_name":"Universit\u00e9 Savoie Mont Blanc","host_organization_lineage":["https://openalex.org/I70900168"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6315407608","display_name":null,"funder_award_id":"G31-4","funder_id":"https://openalex.org/F4320323873","funder_display_name":"Uniwersytet Warszawski"}],"funders":[{"id":"https://openalex.org/F4320323873","display_name":"Uniwersytet Warszawski","ror":"https://ror.org/039bjqg32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2321816919.pdf","grobid_xml":"https://content.openalex.org/works/W2321816919.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1579451758","https://openalex.org/W1964898863","https://openalex.org/W1968365826","https://openalex.org/W1971438970","https://openalex.org/W1977573421","https://openalex.org/W1983167449","https://openalex.org/W1988555400","https://openalex.org/W1996451542","https://openalex.org/W2000206209","https://openalex.org/W2009208085","https://openalex.org/W2013919684","https://openalex.org/W2015611931","https://openalex.org/W2021534482","https://openalex.org/W2022148626","https://openalex.org/W2023638011","https://openalex.org/W2025777803","https://openalex.org/W2029667189","https://openalex.org/W2031599199","https://openalex.org/W2039200346","https://openalex.org/W2043425110","https://openalex.org/W2044002262","https://openalex.org/W2051962390","https://openalex.org/W2069002950","https://openalex.org/W2069168271","https://openalex.org/W2072683434","https://openalex.org/W2074548129","https://openalex.org/W2075590188","https://openalex.org/W2077100489","https://openalex.org/W2083734806","https://openalex.org/W2084719032","https://openalex.org/W2095128344","https://openalex.org/W2111732286","https://openalex.org/W2120406088","https://openalex.org/W2128429826","https://openalex.org/W2130479394","https://openalex.org/W2131288855","https://openalex.org/W2135639356","https://openalex.org/W2143407915","https://openalex.org/W2143867657","https://openalex.org/W2152605692","https://openalex.org/W2156886482","https://openalex.org/W2170554218","https://openalex.org/W2311078281","https://openalex.org/W2327389004"],"related_works":["https://openalex.org/W2185501082","https://openalex.org/W2323894851","https://openalex.org/W1968320918","https://openalex.org/W2032018592","https://openalex.org/W1989882739","https://openalex.org/W2122416619","https://openalex.org/W2074477570","https://openalex.org/W2077003981","https://openalex.org/W2077852446","https://openalex.org/W2089376663"],"abstract_inverted_index":{"Understanding":[0],"the":[1,22,32,52,62,67,70,78,91,100,112,121,125,137,146,154,164,168,182],"interactions":[2],"which":[3],"govern":[4],"aminoglycoside":[5,106,115,141],"antibiotic":[6,126],"binding":[7,107,129],"to":[8,13,43,108],"ribosomal":[9],"RNA":[10,46,109],"is":[11],"essential":[12],"propose":[14],"modifications":[15],"of":[16,31,54,69,114,124,139,148,161,170,184],"these":[17],"antibiotics.":[18],"We":[19,97,134],"have":[20],"investigated":[21,136],"hydrogen":[23,63],"bond":[24],"patterns,":[25],"solvent":[26],"accessibility,":[27],"and":[28,72,82,95,150,180],"stacking":[29],"energies":[30,131],"nucleobases":[33],"in":[34,61,66,77],"twelve":[35],"different":[36],"aminoglycoside-RNA":[37],"crystal":[38],"complexes.":[39],"These":[40],"analyses":[41],"pointed":[42],"some":[44],"antibiotic-induced":[45],"structural":[47],"differences":[48,59],"that":[49,87,99],"depend":[50],"on":[51,153,176],"type":[53],"bound":[55],"aminoglycoside.":[56],"The":[57,85,159],"largest":[58],"were":[60,90],"bonding":[64],"pattern":[65],"vicinity":[68],"U1406":[71],"U1495":[73],"base":[74],"pairs,":[75],"especially":[76],"complexes":[79,86],"with":[80,93,111,120,163],"geneticin":[81],"modified":[83],"paromomycin.":[84],"stand":[88],"out":[89],"ones":[92],"neamine":[94],"kanamycin.":[96],"found":[98],"solvent-accessible":[101],"surface":[102],"area":[103],"buried":[104],"upon":[105],"increases":[110],"number":[113,147],"rings":[116,149],"but":[117],"its":[118],"correlation":[119,160],"net":[122],"charge":[123,166],"or":[127],"experimental":[128,177],"free":[130],"was":[132,181],"weak.":[133],"also":[135],"dependence":[138],"other":[140],"characterizing":[142],"descriptors,":[143],"such":[144],"as":[145],"total":[151,165],"charge,":[152],"experimentally":[155],"determined":[156],"Gibbs":[157],"energies.":[158],"\u0394G":[162],"had":[167],"coefficient":[169],"determination":[171],"R2":[172],"over":[173],"0.8\u20130.9,":[174],"depending":[175],"data":[178],"set,":[179],"highest":[183],"all":[185],"descriptors.":[186]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-22T07:34:49.880490","created_date":"2025-10-10T00:00:00"}
