{"id":"https://openalex.org/W4410542651","doi":"https://doi.org/10.1021/acs.jcim.5c00442","title":"Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?","display_name":"Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?","publication_year":2025,"publication_date":"2025-05-20","ids":{"openalex":"https://openalex.org/W4410542651","doi":"https://doi.org/10.1021/acs.jcim.5c00442","pmid":"https://pubmed.ncbi.nlm.nih.gov/40392062"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00442","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00442","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":"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":"review","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.5c00442","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042085959","display_name":"Mawuli Deegbey","orcid":"https://orcid.org/0000-0003-4478-3353"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mawuli Deegbey","raw_affiliation_strings":["Department of Chemistry","Macromolecules Innovation Institute","Virginia Tech"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"Macromolecules Innovation Institute","institution_ids":[]},{"raw_affiliation_string":"Virginia Tech","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041584086","display_name":"Ethan W. Sumner","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ethan W. Sumner","raw_affiliation_strings":["Department of Chemistry","Macromolecules Innovation Institute","Virginia Tech"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"Macromolecules Innovation Institute","institution_ids":[]},{"raw_affiliation_string":"Virginia Tech","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055958465","display_name":"Valerie Vaissier Welborn","orcid":"https://orcid.org/0000-0003-0834-4441"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Valerie Vaissier Welborn","raw_affiliation_strings":["Department of Chemistry","Macromolecules Innovation Institute","Virginia Tech"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"Macromolecules Innovation Institute","institution_ids":[]},{"raw_affiliation_string":"Virginia Tech","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5055958465"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":3.1568,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.91459386,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"65","issue":"11","first_page":"5289","last_page":"5300"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991999864578247,"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":0.9991999864578247,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12964","display_name":"Diet, Metabolism, and Disease","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/2712","display_name":"Endocrinology, Diabetes and Metabolism"},"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/amoeba","display_name":"Amoeba (genus)","score":0.7425777912139893},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6264248490333557},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.6230310797691345},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.5696356892585754},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5006654262542725},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3737271726131439},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.34612828493118286},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.32121023535728455},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3086104989051819},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.26302558183670044},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25391992926597595},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.2027268409729004},{"id":"https://openalex.org/keywords/microbiology","display_name":"Microbiology","score":0.16180092096328735},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15258681774139404},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14069879055023193}],"concepts":[{"id":"https://openalex.org/C2776172558","wikidata":"https://www.wikidata.org/wiki/Q46729","display_name":"Amoeba (genus)","level":2,"score":0.7425777912139893},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6264248490333557},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.6230310797691345},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5696356892585754},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5006654262542725},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3737271726131439},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.34612828493118286},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.32121023535728455},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3086104989051819},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.26302558183670044},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25391992926597595},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.2027268409729004},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.16180092096328735},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15258681774139404},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14069879055023193},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002236","descriptor_name":"Carbohydrate Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002236","descriptor_name":"Carbohydrate Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002236","descriptor_name":"Carbohydrate Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002236","descriptor_name":"Carbohydrate Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002236","descriptor_name":"Carbohydrate Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002241","descriptor_name":"Carbohydrates","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002241","descriptor_name":"Carbohydrates","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002241","descriptor_name":"Carbohydrates","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002241","descriptor_name":"Carbohydrates","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002241","descriptor_name":"Carbohydrates","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","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},{"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.5c00442","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00442","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":"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:40392062","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40392062","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:12152942","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12152942","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 Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.5c00442","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00442","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":"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":[],"awards":[{"id":"https://openalex.org/G3089970415","display_name":null,"funder_award_id":"DMR-1933525","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6249313196","display_name":null,"funder_award_id":"R35-GM150409","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":128,"referenced_works":["https://openalex.org/W1164593515","https://openalex.org/W1521717899","https://openalex.org/W1537479324","https://openalex.org/W1930867640","https://openalex.org/W1949518151","https://openalex.org/W1964536616","https://openalex.org/W1964773780","https://openalex.org/W1965761289","https://openalex.org/W1968704773","https://openalex.org/W1968861067","https://openalex.org/W1969604945","https://openalex.org/W1973863628","https://openalex.org/W1976094278","https://openalex.org/W1976223991","https://openalex.org/W1976499671","https://openalex.org/W1979046104","https://openalex.org/W1980523613","https://openalex.org/W1981338975","https://openalex.org/W1982414593","https://openalex.org/W1984900762","https://openalex.org/W1990871455","https://openalex.org/W1991297990","https://openalex.org/W1993299482","https://openalex.org/W1999614479","https://openalex.org/W2000456051","https://openalex.org/W2002059603","https://openalex.org/W2003486115","https://openalex.org/W2007528105","https://openalex.org/W2010683382","https://openalex.org/W2016320348","https://openalex.org/W2017472829","https://openalex.org/W2019287938","https://openalex.org/W2020943012","https://openalex.org/W2021778482","https://openalex.org/W2028819452","https://openalex.org/W2030374016","https://openalex.org/W2031321978","https://openalex.org/W2032842297","https://openalex.org/W2033268106","https://openalex.org/W2035205695","https://openalex.org/W2036516535","https://openalex.org/W2039752978","https://openalex.org/W2043235908","https://openalex.org/W2045584354","https://openalex.org/W2046880907","https://openalex.org/W2048398687","https://openalex.org/W2056927024","https://openalex.org/W2057709012","https://openalex.org/W2058418512","https://openalex.org/W2061758567","https://openalex.org/W2063300447","https://openalex.org/W2064965194","https://openalex.org/W2066757885","https://openalex.org/W2067361688","https://openalex.org/W2067738594","https://openalex.org/W2067762146","https://openalex.org/W2068692963","https://openalex.org/W2071281986","https://openalex.org/W2072199801","https://openalex.org/W2075093176","https://openalex.org/W2077456478","https://openalex.org/W2078814366","https://openalex.org/W2079372760","https://openalex.org/W2082506053","https://openalex.org/W2083356447","https://openalex.org/W2085271023","https://openalex.org/W2087596773","https://openalex.org/W2087990820","https://openalex.org/W2089179200","https://openalex.org/W2092000998","https://openalex.org/W2093739872","https://openalex.org/W2098269113","https://openalex.org/W2098943363","https://openalex.org/W2107247227","https://openalex.org/W2119921534","https://openalex.org/W2120350614","https://openalex.org/W2137896303","https://openalex.org/W2145215567","https://openalex.org/W2145631950","https://openalex.org/W2147857380","https://openalex.org/W2150675831","https://openalex.org/W2155524113","https://openalex.org/W2156238280","https://openalex.org/W2157320748","https://openalex.org/W2161087912","https://openalex.org/W2162166182","https://openalex.org/W2165234277","https://openalex.org/W2169962366","https://openalex.org/W2171047927","https://openalex.org/W2272982953","https://openalex.org/W2317414542","https://openalex.org/W2319237737","https://openalex.org/W2327587947","https://openalex.org/W2330362920","https://openalex.org/W2332270957","https://openalex.org/W2335110000","https://openalex.org/W2337762266","https://openalex.org/W2338266679","https://openalex.org/W2417751474","https://openalex.org/W2599024824","https://openalex.org/W2790441008","https://openalex.org/W2793340923","https://openalex.org/W2800611996","https://openalex.org/W2800976333","https://openalex.org/W2902763092","https://openalex.org/W2949867270","https://openalex.org/W2951668576","https://openalex.org/W2953230115","https://openalex.org/W2979518191","https://openalex.org/W3011217020","https://openalex.org/W3011495167","https://openalex.org/W3046258786","https://openalex.org/W3128922103","https://openalex.org/W3133498381","https://openalex.org/W3190391670","https://openalex.org/W4205755645","https://openalex.org/W4205772309","https://openalex.org/W4250017645","https://openalex.org/W4253029741","https://openalex.org/W4283782023","https://openalex.org/W4311784632","https://openalex.org/W4385971404","https://openalex.org/W4388458789","https://openalex.org/W4392193585","https://openalex.org/W4392198401","https://openalex.org/W4400485463","https://openalex.org/W4403275960","https://openalex.org/W4404233833"],"related_works":["https://openalex.org/W3127534742","https://openalex.org/W2022269912","https://openalex.org/W2811043963","https://openalex.org/W2161972019","https://openalex.org/W4366465732","https://openalex.org/W4321013117","https://openalex.org/W1773535258","https://openalex.org/W2312858532","https://openalex.org/W1998915375","https://openalex.org/W4386568614"],"abstract_inverted_index":{"Over":[0],"the":[1,11,53,62,76,88,118,143,178,199],"years,":[2],"molecular":[3],"dynamics":[4],"(MD)":[5],"simulations":[6],"have":[7,28,65],"been":[8,66],"employed":[9],"in":[10,37,47,68,81,172],"study":[12],"of":[13,40,55,83,94,145,155,177,204],"carbohydrates,":[14],"with":[15,117],"force":[16,26,72,100,104],"fields":[17,27,73],"such":[18],"as":[19],"CHARMM,":[20],"AMBER/GLYCAM,":[21],"and":[22,32,70,91,132,149,153,165,202,207],"GROMOS.":[23],"Although":[24],"these":[25,205],"achieved":[29],"considerable":[30],"success":[31,171],"played":[33],"a":[34,103,112,122,186],"pivotal":[35],"role":[36],"our":[38],"understanding":[39],"carbohydrate":[41],"chemistry,":[42],"growing":[43],"interest":[44],"has":[45],"emerged":[46],"incorporating":[48],"polarization":[49,133],"effects":[50],"to":[51,74,110],"enhance":[52],"accuracy":[54,80],"simulations.":[56],"In":[57],"this":[58],"perspective,":[59],"we":[60],"contemplate":[61],"advances":[63,193],"that":[64,87,140],"made":[67],"nonpolarizable":[69],"polarizable":[71],"extract":[75],"key":[77],"factors":[78],"controlling":[79],"MD":[82],"carbohydrates.":[84],"We":[85,138],"find":[86,139],"extreme":[89],"hydrophilicity":[90],"conformational":[92,163],"flexibility":[93,164],"carbohydrates":[95,108],"pose":[96],"challenges":[97],"for":[98,107,162,189],"most":[99],"fields.":[101],"Overall,":[102],"field":[105],"suited":[106],"needs":[109],"include":[111],"water":[113,183],"model":[114,184],"developed":[115],"consistently":[116],"solute":[119],"parameter":[120],"sets,":[121],"soft":[123],"van":[124],"der":[125],"Waals":[126],"repulsion":[127],"term":[128],"at":[129],"short":[130],"distances,":[131],"(whether":[134],"implicit":[135],"or":[136,182],"explicit).":[137],"AMOEBA":[141],"improves":[142],"prediction":[144],"hydration":[146],"shell":[147],"structure":[148],"dynamics,":[150,201],"hydrogen":[151],"bonding,":[152],"kinetics":[154],"diffusion,":[156],"although":[157],"it":[158],"remains":[159],"largely":[160],"untested":[161],"glycosidic":[166],"linkages.":[167],"Nevertheless,":[168],"AMOEBA's":[169],"recent":[170],"modeling":[173],"monosaccharides":[174],"without":[175],"revisions":[176],"potential":[179],"energy":[180],"functions":[181],"presents":[185],"promising":[187],"avenue":[188],"future":[190],"research.":[191],"Such":[192],"will":[194],"provide":[195],"deeper":[196],"insights":[197],"into":[198],"structure,":[200],"interactions":[203],"biologically":[206],"industrially":[208],"relevant":[209],"macromolecules.":[210]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-02T15:55:50.835912","created_date":"2025-10-10T00:00:00"}