{"id":"https://openalex.org/W4298125153","doi":"https://doi.org/10.1021/acs.jcim.2c01049","title":"Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans","display_name":"Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans","publication_year":2022,"publication_date":"2022-09-30","ids":{"openalex":"https://openalex.org/W4298125153","doi":"https://doi.org/10.1021/acs.jcim.2c01049","pmid":"https://pubmed.ncbi.nlm.nih.gov/36179122"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c01049","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01049","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034922405","display_name":"Isabell Louise Grothaus","orcid":"https://orcid.org/0000-0002-0441-3860"},"institutions":[{"id":"https://openalex.org/I180437899","display_name":"University of Bremen","ror":"https://ror.org/04ers2y35","country_code":"DE","type":"education","lineage":["https://openalex.org/I180437899"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Isabell Louise Grothaus","raw_affiliation_strings":["Hybrid Materials Interfaces Group, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359Bremen, Germany"],"raw_orcid":"https://orcid.org/0000-0002-0441-3860","affiliations":[{"raw_affiliation_string":"Hybrid Materials Interfaces Group, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359Bremen, Germany","institution_ids":["https://openalex.org/I180437899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005340330","display_name":"Giovanni Bussi","orcid":"https://orcid.org/0000-0001-9216-5782"},"institutions":[{"id":"https://openalex.org/I138549579","display_name":"Scuola Internazionale Superiore di Studi Avanzati","ror":"https://ror.org/004fze387","country_code":"IT","type":"education","lineage":["https://openalex.org/I138549579"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giovanni Bussi","raw_affiliation_strings":["Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136Trieste, Italy"],"raw_orcid":"https://orcid.org/0000-0001-9216-5782","affiliations":[{"raw_affiliation_string":"Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136Trieste, Italy","institution_ids":["https://openalex.org/I138549579"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074814650","display_name":"Lucio Colombi Ciacchi","orcid":"https://orcid.org/0000-0003-1444-9733"},"institutions":[{"id":"https://openalex.org/I180437899","display_name":"University of Bremen","ror":"https://ror.org/04ers2y35","country_code":"DE","type":"education","lineage":["https://openalex.org/I180437899"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Lucio Colombi Ciacchi","raw_affiliation_strings":["Hybrid Materials Interfaces Group, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359Bremen, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1444-9733","affiliations":[{"raw_affiliation_string":"Hybrid Materials Interfaces Group, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359Bremen, Germany","institution_ids":["https://openalex.org/I180437899"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5074814650"],"corresponding_institution_ids":["https://openalex.org/I180437899"],"apc_list":null,"apc_paid":null,"fwci":0.8664,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.71547689,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"62","issue":"20","first_page":"4992","last_page":"5008"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","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/T10602","display_name":"Glycosylation and Glycoproteins Research","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/T10835","display_name":"Carbohydrate Chemistry and Synthesis","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9979000091552734,"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/conformational-isomerism","display_name":"Conformational isomerism","score":0.7756723165512085},{"id":"https://openalex.org/keywords/glycan","display_name":"Glycan","score":0.6293727159500122},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5459699630737305},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"Conformational ensembles","score":0.4589768946170807},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4526921212673187},{"id":"https://openalex.org/keywords/glycosidic-bond","display_name":"Glycosidic bond","score":0.4147745370864868},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3701595962047577},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.16606354713439941}],"concepts":[{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.7756723165512085},{"id":"https://openalex.org/C206212055","wikidata":"https://www.wikidata.org/wiki/Q2553138","display_name":"Glycan","level":3,"score":0.6293727159500122},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5459699630737305},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.4589768946170807},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4526921212673187},{"id":"https://openalex.org/C150487720","wikidata":"https://www.wikidata.org/wiki/Q422553","display_name":"Glycosidic bond","level":3,"score":0.4147745370864868},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3701595962047577},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.16606354713439941},{"id":"https://openalex.org/C108625454","wikidata":"https://www.wikidata.org/wiki/Q187126","display_name":"Glycoprotein","level":2,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D008358","descriptor_name":"Mannose","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008358","descriptor_name":"Mannose","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008358","descriptor_name":"Mannose","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011908","descriptor_name":"Rationalization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011908","descriptor_name":"Rationalization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011908","descriptor_name":"Rationalization","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":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","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":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.2c01049","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01049","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:36179122","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36179122","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 chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Peace, Justice and strong institutions","score":0.550000011920929,"id":"https://metadata.un.org/sdg/16"}],"awards":[{"id":"https://openalex.org/G1175918770","display_name":null,"funder_award_id":"hbb00001","funder_id":"https://openalex.org/F2827484126","funder_display_name":"Norddeutscher Verbund f\u00fcr Hoch- und H\u00f6chstleistungsrechnen"}],"funders":[{"id":"https://openalex.org/F2827484126","display_name":"Norddeutscher Verbund f\u00fcr Hoch- und H\u00f6chstleistungsrechnen","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":94,"referenced_works":["https://openalex.org/W21784335","https://openalex.org/W53123824","https://openalex.org/W302737051","https://openalex.org/W1031578623","https://openalex.org/W1061146076","https://openalex.org/W1964911318","https://openalex.org/W1967126372","https://openalex.org/W1969017401","https://openalex.org/W1969493239","https://openalex.org/W1970108540","https://openalex.org/W1976223991","https://openalex.org/W1976499671","https://openalex.org/W1980782498","https://openalex.org/W1981338975","https://openalex.org/W1982414593","https://openalex.org/W1984481443","https://openalex.org/W1985944495","https://openalex.org/W1985986368","https://openalex.org/W1990719397","https://openalex.org/W1993177346","https://openalex.org/W1993436046","https://openalex.org/W1995907662","https://openalex.org/W1998329666","https://openalex.org/W2002664623","https://openalex.org/W2006554089","https://openalex.org/W2013937866","https://openalex.org/W2016628249","https://openalex.org/W2021268536","https://openalex.org/W2021520922","https://openalex.org/W2027408247","https://openalex.org/W2033268106","https://openalex.org/W2035087875","https://openalex.org/W2038458884","https://openalex.org/W2039752978","https://openalex.org/W2040809566","https://openalex.org/W2041652966","https://openalex.org/W2049902088","https://openalex.org/W2057477511","https://openalex.org/W2057806291","https://openalex.org/W2064388657","https://openalex.org/W2066375534","https://openalex.org/W2067174909","https://openalex.org/W2073647353","https://openalex.org/W2075620734","https://openalex.org/W2079438618","https://openalex.org/W2085271023","https://openalex.org/W2096512472","https://openalex.org/W2098943363","https://openalex.org/W2112154906","https://openalex.org/W2128572087","https://openalex.org/W2130646807","https://openalex.org/W2136834921","https://openalex.org/W2146411229","https://openalex.org/W2151260212","https://openalex.org/W2278367844","https://openalex.org/W2279717993","https://openalex.org/W2293006210","https://openalex.org/W2317414542","https://openalex.org/W2328132257","https://openalex.org/W2332335459","https://openalex.org/W2507509061","https://openalex.org/W2555870966","https://openalex.org/W2558826010","https://openalex.org/W2586088120","https://openalex.org/W2599024824","https://openalex.org/W2605919772","https://openalex.org/W2608898724","https://openalex.org/W2616506953","https://openalex.org/W2623296956","https://openalex.org/W2807260494","https://openalex.org/W2885359695","https://openalex.org/W2913977622","https://openalex.org/W2921437380","https://openalex.org/W2944129819","https://openalex.org/W2952085518","https://openalex.org/W2953016572","https://openalex.org/W2964095333","https://openalex.org/W2973252091","https://openalex.org/W3045624638","https://openalex.org/W3088579397","https://openalex.org/W3094407181","https://openalex.org/W3100749480","https://openalex.org/W3105901899","https://openalex.org/W3124583009","https://openalex.org/W3133498381","https://openalex.org/W3135452033","https://openalex.org/W3138548040","https://openalex.org/W3162916603","https://openalex.org/W3195039506","https://openalex.org/W4205772309","https://openalex.org/W4206545013","https://openalex.org/W4220663518","https://openalex.org/W4283070732","https://openalex.org/W4292023222"],"related_works":["https://openalex.org/W2023036309","https://openalex.org/W1972863456","https://openalex.org/W2089371831","https://openalex.org/W4385077663","https://openalex.org/W2052399476","https://openalex.org/W2077273959","https://openalex.org/W2810163160","https://openalex.org/W4231449543","https://openalex.org/W1800002986","https://openalex.org/W2610329791"],"abstract_inverted_index":{"Despite":[0],"their":[1,13],"fundamental":[2],"biological":[3],"relevance,":[4],"structure\u2013property":[5],"relationships":[6],"in":[7,36,46,91,167],"N-glycans":[8],"are":[9,42,82,140],"fundamentally":[10],"lacking,":[11],"and":[12,17,31,62,84,126,163,173,181],"highly":[14],"multidimensional":[15],"compositional":[16],"conformational":[18,88,121,171],"phase":[19],"spaces":[20],"remain":[21],"largely":[22],"unexplored.":[23],"The":[24,154],"torsional":[25,180],"flexibility":[26],"of":[27,75,116,123,133,146,161,184],"the":[28,32,114,120,130,143,158,179],"glycosidic":[29],"linkages":[30],"ring":[33],"dynamics":[34,48],"result":[35],"wide,":[37],"rugged":[38],"free-energy":[39,89],"landscapes":[40],"that":[41,52,102,186],"difficult":[43],"to":[44,86,112],"sample":[45],"molecular":[47],"simulations.":[49],"We":[50],"show":[51],"a":[53],"novel":[54],"enhanced-sampling":[55],"scheme":[56,101],"combining":[57],"replica":[58],"exchange":[59],"with":[60,95],"solute":[61],"collective-variable":[63],"tempering,":[64],"enabling":[65],"transitions":[66],"over":[67],"all":[68],"relevant":[69],"energy":[70],"barriers,":[71],"delivers":[72],"converged":[73],"distributions":[74],"solvated":[76],"N-glycan":[77],"conformers.":[78],"Several":[79],"dimensionality-reduction":[80],"algorithms":[81],"compared":[83],"employed":[85],"generate":[87],"maps":[90],"two":[92,134],"dimensions.":[93],"Together":[94],"an":[96,175],"originally":[97],"developed":[98],"conformation-based":[99],"nomenclature":[100],"uniquely":[103],"identifies":[104],"glycan":[105,137],"conformers,":[106],"our":[107],"modeling":[108],"procedure":[109],"is":[110],"applied":[111],"reveal":[113],"effect":[115],"chemical":[117],"substitutions":[118],"on":[119],"ensemble":[122],"selected":[124],"high-mannose-type":[125],"complex":[127],"glycans.":[128],"Moreover,":[129],"structure-prediction":[131],"capabilities":[132],"commonly":[135],"used":[136],"force":[138],"fields":[139],"assessed":[141],"via":[142],"theoretical":[144],"prediction":[145],"experimentally":[147],"available":[148],"nuclear":[149],"magnetic":[150],"resonance":[151],"J-coupling":[152],"constants.":[153],"results":[155],"especially":[156],"confirm":[157],"key":[159],"role":[160],"\u03c9":[162],"\u03c8":[164],"torsion":[165],"angles":[166],"discriminating":[168],"between":[169,178],"different":[170],"states":[172],"suggest":[174],"intriguing":[176],"correlation":[177],"ring-puckering":[182],"degrees":[183],"freedom":[185],"may":[187],"be":[188],"biologically":[189],"relevant.":[190]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
