{"id":"https://openalex.org/W2594441115","doi":"https://doi.org/10.1021/acs.jcim.6b00595","title":"Comparison of Implicit and Explicit Solvation Models for<i>Iota</i>-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics","display_name":"Comparison of Implicit and Explicit Solvation Models for<i>Iota</i>-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics","publication_year":2017,"publication_date":"2017-03-08","ids":{"openalex":"https://openalex.org/W2594441115","doi":"https://doi.org/10.1021/acs.jcim.6b00595","mag":"2594441115","pmid":"https://pubmed.ncbi.nlm.nih.gov/28271890"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00595","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00595","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/A5008319808","display_name":"Wasinee Khuntawee","orcid":"https://orcid.org/0000-0002-7439-9590"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Wasinee Khuntawee","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065269033","display_name":"Manaschai Kunaseth","orcid":"https://orcid.org/0000-0002-1327-2502"},"institutions":[{"id":"https://openalex.org/I1332092204","display_name":"National Science and Technology Development Agency","ror":"https://ror.org/04vy95b61","country_code":"TH","type":"government","lineage":["https://openalex.org/I1332092204"]},{"id":"https://openalex.org/I4210107674","display_name":"National Nanotechnology Center","ror":"https://ror.org/01neh8064","country_code":"TH","type":"facility","lineage":["https://openalex.org/I1332092204","https://openalex.org/I4210107674"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Manaschai Kunaseth","raw_affiliation_strings":["National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand"],"raw_orcid":"https://orcid.org/0000-0002-1327-2502","affiliations":[{"raw_affiliation_string":"National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand","institution_ids":["https://openalex.org/I4210107674","https://openalex.org/I1332092204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027071305","display_name":"Chompoonut Rungnim","orcid":"https://orcid.org/0000-0002-2794-5253"},"institutions":[{"id":"https://openalex.org/I1332092204","display_name":"National Science and Technology Development Agency","ror":"https://ror.org/04vy95b61","country_code":"TH","type":"government","lineage":["https://openalex.org/I1332092204"]},{"id":"https://openalex.org/I4210107674","display_name":"National Nanotechnology Center","ror":"https://ror.org/01neh8064","country_code":"TH","type":"facility","lineage":["https://openalex.org/I1332092204","https://openalex.org/I4210107674"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Chompoonut Rungnim","raw_affiliation_strings":["National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand","institution_ids":["https://openalex.org/I4210107674","https://openalex.org/I1332092204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045091573","display_name":"Suradej Intagorn","orcid":null},"institutions":[{"id":"https://openalex.org/I198105771","display_name":"Kasetsart University","ror":"https://ror.org/05gzceg21","country_code":"TH","type":"education","lineage":["https://openalex.org/I198105771"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Suradej Intagorn","raw_affiliation_strings":["Department of Mathematics, Statistics and Computer Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Statistics and Computer Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand","institution_ids":["https://openalex.org/I198105771"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027316413","display_name":"Peter Wolschann","orcid":"https://orcid.org/0000-0001-6104-6596"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Peter Wolschann","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026065355","display_name":"Nawee Kungwan","orcid":"https://orcid.org/0000-0002-2960-6853"},"institutions":[{"id":"https://openalex.org/I48076826","display_name":"Chiang Mai University","ror":"https://ror.org/05m2fqn25","country_code":"TH","type":"education","lineage":["https://openalex.org/I48076826"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Nawee Kungwan","raw_affiliation_strings":["Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Muang District, Chiang Mai 50200, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Muang District, Chiang Mai 50200, Thailand","institution_ids":["https://openalex.org/I48076826"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031067302","display_name":"Thanyada Rungrotmongkol","orcid":"https://orcid.org/0000-0002-7402-3235"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Thanyada Rungrotmongkol","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5020458772","display_name":"Supot Hannongbua","orcid":"https://orcid.org/0000-0001-9008-2748"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Supot Hannongbua","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5008319808"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.5615,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.65537639,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"57","issue":"4","first_page":"778","last_page":"786"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9890999794006348,"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":0.9890999794006348,"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":0.9843999743461609,"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/T12192","display_name":"Polysaccharides Composition and Applications","score":0.9678000211715698,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.7772325277328491},{"id":"https://openalex.org/keywords/solvation","display_name":"Solvation","score":0.7687392830848694},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.664313018321991},{"id":"https://openalex.org/keywords/glycosidic-bond","display_name":"Glycosidic bond","score":0.5587037205696106},{"id":"https://openalex.org/keywords/water-model","display_name":"Water model","score":0.4425656795501709},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.42142558097839355},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.36534789204597473},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.3488025963306427},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.1881369948387146},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.1049843430519104}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7772325277328491},{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.7687392830848694},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.664313018321991},{"id":"https://openalex.org/C150487720","wikidata":"https://www.wikidata.org/wiki/Q422553","display_name":"Glycosidic bond","level":3,"score":0.5587037205696106},{"id":"https://openalex.org/C119049451","wikidata":"https://www.wikidata.org/wiki/Q3318070","display_name":"Water model","level":3,"score":0.4425656795501709},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.42142558097839355},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.36534789204597473},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.3488025963306427},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.1881369948387146},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.1049843430519104},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"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":"D003505","descriptor_name":"Cyclodextrins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003505","descriptor_name":"Cyclodextrins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003505","descriptor_name":"Cyclodextrins","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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","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":"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":2,"locations":[{"id":"doi:10.1021/acs.jcim.6b00595","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00595","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:28271890","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28271890","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":"Clean water and sanitation","id":"https://metadata.un.org/sdg/6","score":0.6499999761581421}],"awards":[{"id":"https://openalex.org/G441043072","display_name":null,"funder_award_id":"RSA5980069","funder_id":"https://openalex.org/F4320322614","funder_display_name":"Thailand Research Fund"},{"id":"https://openalex.org/G4991531966","display_name":null,"funder_award_id":"IRG5780008","funder_id":"https://openalex.org/F4320322614","funder_display_name":"Thailand Research Fund"}],"funders":[{"id":"https://openalex.org/F4320322614","display_name":"Thailand Research Fund","ror":"https://ror.org/03gd1bh37"},{"id":"https://openalex.org/F4320322817","display_name":"National Research Council of Thailand","ror":"https://ror.org/018wfhg78"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W331776414","https://openalex.org/W1560481517","https://openalex.org/W1953984262","https://openalex.org/W1963481573","https://openalex.org/W1964672234","https://openalex.org/W1966703669","https://openalex.org/W1976124127","https://openalex.org/W1987833947","https://openalex.org/W1990517428","https://openalex.org/W1998844503","https://openalex.org/W2009086942","https://openalex.org/W2021042085","https://openalex.org/W2032363535","https://openalex.org/W2036732534","https://openalex.org/W2040809566","https://openalex.org/W2049633694","https://openalex.org/W2092192536","https://openalex.org/W2100627460","https://openalex.org/W2106683459","https://openalex.org/W2148994928","https://openalex.org/W2322308883","https://openalex.org/W2334841042","https://openalex.org/W2417162538","https://openalex.org/W2422799170","https://openalex.org/W2526026731","https://openalex.org/W2562618250","https://openalex.org/W2949498440","https://openalex.org/W2998144848","https://openalex.org/W3004982183","https://openalex.org/W3104163644","https://openalex.org/W4236463595"],"related_works":["https://openalex.org/W3175840220","https://openalex.org/W2049601662","https://openalex.org/W2062824236","https://openalex.org/W1966675092","https://openalex.org/W2298224373","https://openalex.org/W2116698685","https://openalex.org/W2018007656","https://openalex.org/W3190044890","https://openalex.org/W2063463219","https://openalex.org/W4221044347"],"abstract_inverted_index":{"Large":[0],"ring":[1],"cyclodextrins":[2],"have":[3,15],"become":[4],"increasingly":[5],"important":[6],"for":[7,200],"drug":[8],"delivery":[9],"applications.":[10],"In":[11,104,126],"this":[12],"work,":[13],"we":[14],"performed":[16],"replica-exchange":[17],"molecular":[18,201],"dynamics":[19],"simulations":[20],"using":[21,132],"both":[22],"implicit":[23,74,145],"and":[24,56,67,92,178,193],"explicit":[25,109,163],"water":[26,75,110,146],"solvation":[27,111,191],"models":[28],"to":[29,51,151,157],"study":[30],"the":[31,53,152,175,205],"conformational":[32],"diversity":[33],"of":[34,59,63,88,100,118,129,141,171,190],"iota-cyclodextrin":[35],"containing":[36],"14":[37],"\u03b1-1,4":[38],"glycosidic":[39],"linked":[40],"d-glucopyranose":[41],"units":[42],"(CD14).":[43],"The":[44],"new":[45,196],"quantifiable":[46,197],"calculation":[47],"methods":[48],"are":[49,124],"proposed":[50],"analyze":[52],"openness,":[54],"bending,":[55],"twisted":[57,114,160,179],"conformation":[58,69,84,202],"CD14":[60,71,106,130,143,172,187],"in":[61,72,81,107,144,155,159,162,204],"terms":[62],"circularity,":[64],"biplanar":[65,98],"angle,":[66],"one-directional":[68],"(ODC).":[70],"GB":[73],"model":[76,136],"(Igb5)":[77],"was":[78],"found":[79],"mostly":[80],"an":[82],"opened":[83],"with":[85,96,115],"average":[86,97,116],"circularity":[87,117],"0.39":[89],"\u00b1":[90,102,120],"0.16":[91,119],"a":[93,133],"slight":[94],"bend":[95],"angle":[99],"145.5":[101],"16.0\u00b0.":[103],"contrast,":[105],"TIP3P":[108],"is":[112],"significantly":[113],"0.10,":[121],"while":[122],"29.1%":[123],"ODCs.":[125],"addition,":[127],"classification":[128],"conformations":[131,170],"Gaussian":[134],"mixture":[135],"(GMM)":[137],"shows":[138],"that":[139],"85.0%":[140],"all":[142],"at":[147],"300":[148],"K":[149],"correspond":[150],"elliptical":[153],"conformation,":[154,188],"contrast":[156],"82.3%":[158],"form":[161],"water.":[164],"GMM":[165],"clustering":[166],"also":[167,194],"reveals":[168],"minority":[169],"such":[173],"as":[174],"8-shape,":[176],"boat-form,":[177],"conformations.":[180],"This":[181],"work":[182],"provides":[183],"fundamental":[184],"insights":[185],"into":[186],"influence":[189],"models,":[192],"proposes":[195],"analysis":[198],"techniques":[199],"studies":[203],"future.":[206]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2017-03-16T00:00:00"}
