{"id":"https://openalex.org/W3176594870","doi":"https://doi.org/10.1021/acs.jcim.1c00339","title":"Force Field Benchmark of Amino Acids. 3. Hydration with Scaled Lennard-Jones Interactions","display_name":"Force Field Benchmark of Amino Acids. 3. Hydration with Scaled Lennard-Jones Interactions","publication_year":2021,"publication_date":"2021-06-29","ids":{"openalex":"https://openalex.org/W3176594870","doi":"https://doi.org/10.1021/acs.jcim.1c00339","mag":"3176594870","pmid":"https://pubmed.ncbi.nlm.nih.gov/34185520"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c00339","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00339","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/A5075968874","display_name":"Yejie Qiu","orcid":"https://orcid.org/0000-0001-6341-4671"},"institutions":[{"id":"https://openalex.org/I92403157","display_name":"University of Science and Technology Beijing","ror":"https://ror.org/02egmk993","country_code":"CN","type":"education","lineage":["https://openalex.org/I92403157"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yejie Qiu","raw_affiliation_strings":["Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China"],"raw_orcid":"https://orcid.org/0000-0001-6341-4671","affiliations":[{"raw_affiliation_string":"Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China","institution_ids":["https://openalex.org/I92403157"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016132190","display_name":"Wenjie Shan","orcid":"https://orcid.org/0000-0001-5724-4805"},"institutions":[{"id":"https://openalex.org/I92403157","display_name":"University of Science and Technology Beijing","ror":"https://ror.org/02egmk993","country_code":"CN","type":"education","lineage":["https://openalex.org/I92403157"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenjie Shan","raw_affiliation_strings":["Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China","institution_ids":["https://openalex.org/I92403157"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063889804","display_name":"Haiyang Zhang","orcid":"https://orcid.org/0000-0002-2410-7078"},"institutions":[{"id":"https://openalex.org/I92403157","display_name":"University of Science and Technology Beijing","ror":"https://ror.org/02egmk993","country_code":"CN","type":"education","lineage":["https://openalex.org/I92403157"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Haiyang Zhang","raw_affiliation_strings":["Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-2410-7078","affiliations":[{"raw_affiliation_string":"Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China","institution_ids":["https://openalex.org/I92403157"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5063889804"],"corresponding_institution_ids":["https://openalex.org/I92403157"],"apc_list":null,"apc_paid":null,"fwci":1.2688,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.7936174,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"61","issue":"7","first_page":"3571","last_page":"3582"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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/T10044","display_name":"Protein Structure and Dynamics","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/T11162","display_name":"Enzyme Structure and Function","score":0.9984999895095825,"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/T10474","display_name":"Material Dynamics and Properties","score":0.9926000237464905,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.7091182470321655},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.6582025289535522},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.6482547521591187},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5377588272094727},{"id":"https://openalex.org/keywords/water-model","display_name":"Water model","score":0.5135079026222229},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4824141263961792},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4777878224849701},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.4747253656387329},{"id":"https://openalex.org/keywords/london-dispersion-force","display_name":"London dispersion force","score":0.44889408349990845},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.43815356492996216},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4192315638065338},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.4173644781112671},{"id":"https://openalex.org/keywords/aqueous-solution","display_name":"Aqueous solution","score":0.4102924168109894},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3549084961414337},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3239249587059021},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.28805777430534363},{"id":"https://openalex.org/keywords/van-der-waals-force","display_name":"van der Waals force","score":0.23923134803771973},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1584899127483368},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.1447535753250122},{"id":"https://openalex.org/keywords/physical-chemistry","display_name":"Physical chemistry","score":0.12125781178474426},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.10908010601997375},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07236281037330627}],"concepts":[{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.7091182470321655},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.6582025289535522},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.6482547521591187},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5377588272094727},{"id":"https://openalex.org/C119049451","wikidata":"https://www.wikidata.org/wiki/Q3318070","display_name":"Water model","level":3,"score":0.5135079026222229},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4824141263961792},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4777878224849701},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.4747253656387329},{"id":"https://openalex.org/C185424724","wikidata":"https://www.wikidata.org/wiki/Q519418","display_name":"London dispersion force","level":4,"score":0.44889408349990845},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.43815356492996216},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4192315638065338},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.4173644781112671},{"id":"https://openalex.org/C184651966","wikidata":"https://www.wikidata.org/wiki/Q906356","display_name":"Aqueous solution","level":2,"score":0.4102924168109894},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3549084961414337},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3239249587059021},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.28805777430534363},{"id":"https://openalex.org/C126061179","wikidata":"https://www.wikidata.org/wiki/Q189627","display_name":"van der Waals force","level":3,"score":0.23923134803771973},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1584899127483368},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.1447535753250122},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.12125781178474426},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.10908010601997375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07236281037330627},{"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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":null,"qualifier_name":null,"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":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},{"descriptor_ui":"D064267","descriptor_name":"Intrinsically Disordered Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064267","descriptor_name":"Intrinsically Disordered Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064267","descriptor_name":"Intrinsically Disordered Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.1c00339","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00339","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:34185520","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34185520","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":[{"id":"https://metadata.un.org/sdg/6","display_name":"Clean water and sanitation","score":0.8299999833106995}],"awards":[{"id":"https://openalex.org/G2538394642","display_name":null,"funder_award_id":"21606016","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3536486917","display_name":null,"funder_award_id":"21977013","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":82,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1651084065","https://openalex.org/W1824051645","https://openalex.org/W1911670820","https://openalex.org/W1929341869","https://openalex.org/W1935237622","https://openalex.org/W1968790827","https://openalex.org/W1976499671","https://openalex.org/W1976983810","https://openalex.org/W1978498560","https://openalex.org/W1990536516","https://openalex.org/W2000456051","https://openalex.org/W2002911779","https://openalex.org/W2020555083","https://openalex.org/W2023400093","https://openalex.org/W2023691820","https://openalex.org/W2024726841","https://openalex.org/W2028702957","https://openalex.org/W2031888811","https://openalex.org/W2035687084","https://openalex.org/W2047474238","https://openalex.org/W2047631698","https://openalex.org/W2049475242","https://openalex.org/W2057477511","https://openalex.org/W2060872117","https://openalex.org/W2066690664","https://openalex.org/W2067174909","https://openalex.org/W2070189028","https://openalex.org/W2071827681","https://openalex.org/W2073898109","https://openalex.org/W2075175766","https://openalex.org/W2075369230","https://openalex.org/W2077709135","https://openalex.org/W2081693079","https://openalex.org/W2103945336","https://openalex.org/W2124597092","https://openalex.org/W2128572087","https://openalex.org/W2136219546","https://openalex.org/W2143598945","https://openalex.org/W2154455129","https://openalex.org/W2234602429","https://openalex.org/W2293006210","https://openalex.org/W2307152728","https://openalex.org/W2321195257","https://openalex.org/W2327000477","https://openalex.org/W2327421019","https://openalex.org/W2327566542","https://openalex.org/W2327880765","https://openalex.org/W2328723871","https://openalex.org/W2333133288","https://openalex.org/W2337762266","https://openalex.org/W2404280981","https://openalex.org/W2411580022","https://openalex.org/W2420659973","https://openalex.org/W2519684817","https://openalex.org/W2555870966","https://openalex.org/W2600916235","https://openalex.org/W2754246072","https://openalex.org/W2765209572","https://openalex.org/W2768469871","https://openalex.org/W2768709305","https://openalex.org/W2791904540","https://openalex.org/W2793701070","https://openalex.org/W2797232968","https://openalex.org/W2800697076","https://openalex.org/W2806203702","https://openalex.org/W2884470781","https://openalex.org/W2887958072","https://openalex.org/W2892745578","https://openalex.org/W2902556395","https://openalex.org/W2921063431","https://openalex.org/W2923759574","https://openalex.org/W2962951846","https://openalex.org/W2989052455","https://openalex.org/W3013264144","https://openalex.org/W3030183899","https://openalex.org/W3080264551","https://openalex.org/W3088807402","https://openalex.org/W3105643282","https://openalex.org/W3112712173","https://openalex.org/W3130801441","https://openalex.org/W4243546559"],"related_works":["https://openalex.org/W3127534742","https://openalex.org/W2105451663","https://openalex.org/W2022269912","https://openalex.org/W1966675092","https://openalex.org/W2811043963","https://openalex.org/W2161972019","https://openalex.org/W4366465732","https://openalex.org/W4321013117","https://openalex.org/W2312858532","https://openalex.org/W3015215467"],"abstract_inverted_index":{"Classical":[0],"protein":[1,22,97,181],"force":[2,149,182],"fields":[3,150,183],"were":[4],"reported":[5],"with":[6,161],"too":[7],"weak":[8],"protein\u2013water":[9,141],"interactions":[10,33,95,118,131,142,173,193],"relative":[11],"to":[12,16,83,91,137,157,190,196,199],"protein\u2013protein":[13,117,172],"interactions,":[14],"leading":[15,198],"more":[17,113,139,194],"compact":[18,85],"structures":[19],"and":[20,40,45,67,73,87,98,154,174,184],"artificial":[21],"aggregation.":[23],"Here":[24],"we":[25],"investigated":[26],"the":[27,35,41,71,94,106,121],"impacts":[28],"of":[29,37,43,60,76,180],"scaled":[30],"Lennard-Jones":[31],"(LJ)":[32],"on":[34],"hydration":[36,57],"amino":[38,62],"acids":[39],"simulation":[42],"folded":[44,77],"intrinsically":[46],"disordered":[47],"proteins":[48,78],"(IDPs).":[49],"The":[50,80],"obtained":[51],"optimal":[52],"scaling":[53,81],"parameters":[54],"reproduce":[55],"accurately":[56],"free":[58],"energies":[59],"neutral":[61],"acid":[63],"side":[64],"chain":[65],"analogues":[66],"do":[68],"not":[69],"affect":[70],"compactness":[72],"structural":[74],"stability":[75],"significantly.":[79],"leads":[82],"less":[84],"IDPs":[86],"varies":[88],"from":[89],"case":[90],"case.":[92],"Strengthening":[93],"between":[96,170],"water":[99,159,185],"oxygen":[100],"or":[101,204],"hydrogen":[102],"atoms":[103],"by":[104,119],"increasing":[105],"interacting":[107,122],"LJ":[108],"well":[109,136],"depth":[110],"(\u03b5)":[111],"appears":[112],"effective":[114],"than":[115],"weakening":[116,129],"reducing":[120],"dispersion":[123],"coefficients":[124],"(C6).":[125],"We":[126],"demonstrate":[127],"that":[128],"water\u2013water":[130,163,176],"is":[132,166,187],"a":[133,168],"solution":[134],"as":[135],"obtaining":[138],"favorable":[140],"in":[143],"an":[144],"indirect":[145],"way,":[146],"although":[147],"modern":[148],"like":[151],"Amber":[152],"ff19SB":[153],"a99SB-disp":[155],"tend":[156],"use":[158],"models":[160,186],"strong":[162,171,175],"interactions.":[164,177],"This":[165],"likely":[167],"compromise":[169],"Independent":[178],"optimization":[179],"therefore":[188],"needed":[189],"make":[191],"both":[192],"close":[195],"reality,":[197],"good":[200],"accuracy":[201],"without":[202],"bias":[203],"scaling.":[205]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
