{"id":"https://openalex.org/W4361296857","doi":"https://doi.org/10.1021/acs.jcim.2c01472","title":"Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans","display_name":"Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans","publication_year":2023,"publication_date":"2023-03-29","ids":{"openalex":"https://openalex.org/W4361296857","doi":"https://doi.org/10.1021/acs.jcim.2c01472","pmid":"https://pubmed.ncbi.nlm.nih.gov/36989082"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c01472","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01472","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.2c01472","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.2c01472","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065409464","display_name":"Mateusz Marcisz","orcid":"https://orcid.org/0000-0003-2043-6875"},"institutions":[{"id":"https://openalex.org/I40413290","display_name":"University of Gda\u0144sk","ror":"https://ror.org/011dv8m48","country_code":"PL","type":"education","lineage":["https://openalex.org/I40413290"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Mateusz Marcisz","raw_affiliation_strings":["Faculty of Chemistry, University of Gda\u0144sk, ul. Wita Stwosza 63, 80-308 Gda\u0144sk, Poland","Intercollegiate Faculty of Biotechnology of UG and MUG, ul. Abrahama 58, 80-307 Gda\u0144sk, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Chemistry, University of Gda\u0144sk, ul. Wita Stwosza 63, 80-308 Gda\u0144sk, Poland","institution_ids":["https://openalex.org/I40413290"]},{"raw_affiliation_string":"Intercollegiate Faculty of Biotechnology of UG and MUG, ul. Abrahama 58, 80-307 Gda\u0144sk, Poland","institution_ids":["https://openalex.org/I40413290"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086671958","display_name":"Sergey A. Samsonov","orcid":"https://orcid.org/0000-0002-5166-4849"},"institutions":[{"id":"https://openalex.org/I40413290","display_name":"University of Gda\u0144sk","ror":"https://ror.org/011dv8m48","country_code":"PL","type":"education","lineage":["https://openalex.org/I40413290"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Sergey A. Samsonov","raw_affiliation_strings":["Faculty of Chemistry, University of Gda\u0144sk, ul. Wita Stwosza 63, 80-308 Gda\u0144sk, Poland"],"raw_orcid":"https://orcid.org/0000-0002-5166-4849","affiliations":[{"raw_affiliation_string":"Faculty of Chemistry, University of Gda\u0144sk, ul. Wita Stwosza 63, 80-308 Gda\u0144sk, Poland","institution_ids":["https://openalex.org/I40413290"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5065409464","https://openalex.org/A5086671958"],"corresponding_institution_ids":["https://openalex.org/I40413290"],"apc_list":null,"apc_paid":null,"fwci":2.4113,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.8981178,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"63","issue":"7","first_page":"2147","last_page":"2157"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9998999834060669,"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":0.9998999834060669,"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/T11131","display_name":"Proteoglycans and glycosaminoglycans research","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T12104","display_name":"Protein Tyrosine Phosphatases","score":0.9976999759674072,"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/benchmark","display_name":"Benchmark (surveying)","score":0.7587757110595703},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5660169124603271},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.5242526531219482},{"id":"https://openalex.org/keywords/glycosaminoglycan","display_name":"Glycosaminoglycan","score":0.5053113102912903},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.47283583879470825},{"id":"https://openalex.org/keywords/solvent","display_name":"Solvent","score":0.447131872177124},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40095871686935425},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3505781292915344},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.2881123423576355},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14703112840652466},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1447969377040863},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.13428255915641785}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7587757110595703},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5660169124603271},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5242526531219482},{"id":"https://openalex.org/C153074725","wikidata":"https://www.wikidata.org/wiki/Q407553","display_name":"Glycosaminoglycan","level":2,"score":0.5053113102912903},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.47283583879470825},{"id":"https://openalex.org/C2780471494","wikidata":"https://www.wikidata.org/wiki/Q146505","display_name":"Solvent","level":2,"score":0.447131872177124},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40095871686935425},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3505781292915344},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.2881123423576355},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14703112840652466},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1447969377040863},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.13428255915641785},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006025","descriptor_name":"Glycosaminoglycans","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006025","descriptor_name":"Glycosaminoglycans","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006025","descriptor_name":"Glycosaminoglycans","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006025","descriptor_name":"Glycosaminoglycans","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"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":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","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:10.1021/acs.jcim.2c01472","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01472","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.2c01472","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:36989082","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36989082","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},{"id":"pmh:oai:pubmedcentral.nih.gov:10091405","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10091405","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10091405/pdf/ci2c01472.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":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.2c01472","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01472","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.2c01472","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/6","score":0.7799999713897705,"display_name":"Clean water and sanitation"}],"awards":[{"id":"https://openalex.org/G1551502434","display_name":null,"funder_award_id":"CA18103","funder_id":"https://openalex.org/F4320320366","funder_display_name":"European Cooperation in Science and Technology"},{"id":"https://openalex.org/G240473628","display_name":null,"funder_award_id":"UMO-2018/30/E/ST4/00037","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320320366","display_name":"European Cooperation in Science and Technology","ror":"https://ror.org/01bstzn19"},{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4361296857.pdf","grobid_xml":"https://content.openalex.org/works/W4361296857.grobid-xml"},"referenced_works_count":92,"referenced_works":["https://openalex.org/W1679229092","https://openalex.org/W1840163537","https://openalex.org/W1849896198","https://openalex.org/W1877090369","https://openalex.org/W1965144118","https://openalex.org/W1965504416","https://openalex.org/W1976499671","https://openalex.org/W1983659112","https://openalex.org/W1984406447","https://openalex.org/W1986012385","https://openalex.org/W1988870473","https://openalex.org/W1994974479","https://openalex.org/W1996678638","https://openalex.org/W1997203824","https://openalex.org/W2002746806","https://openalex.org/W2012748696","https://openalex.org/W2019574809","https://openalex.org/W2024726841","https://openalex.org/W2025541110","https://openalex.org/W2025851253","https://openalex.org/W2025880126","https://openalex.org/W2028702957","https://openalex.org/W2032853185","https://openalex.org/W2036484340","https://openalex.org/W2037590307","https://openalex.org/W2043469852","https://openalex.org/W2049475242","https://openalex.org/W2054732153","https://openalex.org/W2055881436","https://openalex.org/W2058052041","https://openalex.org/W2066690664","https://openalex.org/W2069748232","https://openalex.org/W2083519509","https://openalex.org/W2087596773","https://openalex.org/W2092749292","https://openalex.org/W2093049619","https://openalex.org/W2098943363","https://openalex.org/W2101078720","https://openalex.org/W2130479394","https://openalex.org/W2130673759","https://openalex.org/W2145369603","https://openalex.org/W2147805425","https://openalex.org/W2152821878","https://openalex.org/W2153703984","https://openalex.org/W2154019529","https://openalex.org/W2164270482","https://openalex.org/W2231215589","https://openalex.org/W2315436823","https://openalex.org/W2320727223","https://openalex.org/W2329540625","https://openalex.org/W2475616965","https://openalex.org/W2510867035","https://openalex.org/W2582743722","https://openalex.org/W2586101801","https://openalex.org/W2773728373","https://openalex.org/W2790164154","https://openalex.org/W2791422181","https://openalex.org/W2794874901","https://openalex.org/W2800154116","https://openalex.org/W2890624098","https://openalex.org/W2892229044","https://openalex.org/W2894134508","https://openalex.org/W2907733456","https://openalex.org/W2912116791","https://openalex.org/W2914504056","https://openalex.org/W2926834221","https://openalex.org/W2937369800","https://openalex.org/W2954153470","https://openalex.org/W2960448439","https://openalex.org/W2964365474","https://openalex.org/W3008867420","https://openalex.org/W3035593737","https://openalex.org/W3041474915","https://openalex.org/W3048072144","https://openalex.org/W3085153423","https://openalex.org/W3096022792","https://openalex.org/W3105643282","https://openalex.org/W3134015719","https://openalex.org/W3134558668","https://openalex.org/W3137452322","https://openalex.org/W3162024895","https://openalex.org/W3168436232","https://openalex.org/W3168566956","https://openalex.org/W3196695543","https://openalex.org/W3204779422","https://openalex.org/W4200433224","https://openalex.org/W4211225699","https://openalex.org/W4221029688","https://openalex.org/W4280497234","https://openalex.org/W4281675815","https://openalex.org/W4284666358","https://openalex.org/W4285735829"],"related_works":["https://openalex.org/W2032255522","https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2155643123","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W621572675","https://openalex.org/W4246352526"],"abstract_inverted_index":{"In":[0,130],"computational":[1,69,127],"studies":[2],"of":[3,8,24,32,45,71,88,107,110,126],"glycosaminoglycans":[4],"(GAGs),":[5],"a":[6],"group":[7],"anionic,":[9],"periodic":[10],"linear":[11],"polysaccharides,":[12],"so":[13],"far":[14],"there":[15,55],"has":[16],"been":[17],"very":[18],"little":[19],"discussion":[20],"about":[21],"the":[22,28,36,46,68,92,97,103,108,117,146,160,167,170],"role":[23],"solvent":[25,98,143,153,173],"models":[26,51,63,144,154],"in":[27,52,67,105,124,159],"molecular":[29,157,161],"dynamics":[30,162],"simulations":[31],"these":[33],"molecules.":[34],"Predominantly,":[35],"TIP3P":[37],"water":[38,50,62],"model":[39,99],"is":[40,101],"commonly":[41],"used":[42],"as":[43],"one":[44],"most":[47,171],"popular":[48],"explicit":[49,59,142],"general.":[53],"However,":[54],"are":[56,65,76],"numerous":[57],"alternative":[58],"and":[60,82,140,178],"implicit":[61,139],"that":[64,100],"neglected":[66],"research":[70],"GAGs.":[72],"Since":[73],"solvent-mediated":[74],"interactions":[75],"particularly":[77],"important":[78],"for":[79,91,169,175],"GAG":[80,93,113,176],"dynamic":[81],"structural":[83],"properties,":[84],"it":[85],"would":[86,120],"be":[87,121],"great":[89],"interest":[90],"community":[94],"to":[95,148,181,185,187],"establish":[96],"suited":[102],"best":[104],"terms":[106,125],"quality":[109],"theoretically":[111],"obtained":[112],"parameters":[114],"and,":[115],"at":[116],"same":[118],"time,":[119],"reasonably":[122],"demanding":[123],"resources":[128],"required.":[129],"this":[131,188],"study,":[132],"heparin":[133],"(HP)":[134],"was":[135],"simulated":[136],"using":[137],"five":[138],"six":[141],"with":[145],"aim":[147],"find":[149],"out":[150],"how":[151],"different":[152],"influence":[155],"HP's":[156],"descriptors":[158],"simulations.":[163],"Here,":[164],"we":[165,179],"initiate":[166],"search":[168],"appropriate":[172],"representation":[174],"systems":[177],"hope":[180],"encourage":[182],"other":[183],"groups":[184],"contribute":[186],"highly":[189],"relevant":[190],"subject.":[191]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
