{"id":"https://openalex.org/W4280513179","doi":"https://doi.org/10.1021/acs.jcim.2c00066","title":"Development of a Hybrid-Resolution Force Field for Peptide Self-Assembly Simulations: Optimizing Peptide\u2013Peptide and Peptide\u2013Solvent Interactions","display_name":"Development of a Hybrid-Resolution Force Field for Peptide Self-Assembly Simulations: Optimizing Peptide\u2013Peptide and Peptide\u2013Solvent Interactions","publication_year":2022,"publication_date":"2022-05-13","ids":{"openalex":"https://openalex.org/W4280513179","doi":"https://doi.org/10.1021/acs.jcim.2c00066","pmid":"https://pubmed.ncbi.nlm.nih.gov/35561002"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c00066","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00066","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/A5072876713","display_name":"Xiang Cai","orcid":"https://orcid.org/0000-0002-1694-2807"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiang Cai","raw_affiliation_strings":["State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5117823207","display_name":"Wei Han","orcid":"https://orcid.org/0000-0003-0759-1766"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wei Han","raw_affiliation_strings":["Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China","State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China"],"raw_orcid":"https://orcid.org/0000-0003-0759-1766","affiliations":[{"raw_affiliation_string":"Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China","institution_ids":["https://openalex.org/I4210102541"]},{"raw_affiliation_string":"State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5117823207"],"corresponding_institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210102541"],"apc_list":null,"apc_paid":null,"fwci":0.8723,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.68502435,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"62","issue":"11","first_page":"2744","last_page":"2760"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11419","display_name":"Supramolecular Self-Assembly in Materials","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2502","display_name":"Biomaterials"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11419","display_name":"Supramolecular Self-Assembly in Materials","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2502","display_name":"Biomaterials"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9991000294685364,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9990000128746033,"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/peptide","display_name":"Peptide","score":0.8251968026161194},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.606890082359314},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.5318666696548462},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4773730933666229},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.468996524810791},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4262915253639221},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4071711003780365},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.39534619450569153},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.29031747579574585},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.2563628554344177},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.1916201412677765},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1276877522468567},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09921395778656006},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.0830451250076294},{"id":"https://openalex.org/keywords/mechanical-engineering","display_name":"Mechanical engineering","score":0.07389816641807556}],"concepts":[{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.8251968026161194},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.606890082359314},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5318666696548462},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4773730933666229},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.468996524810791},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4262915253639221},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4071711003780365},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.39534619450569153},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.29031747579574585},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.2563628554344177},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.1916201412677765},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1276877522468567},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09921395778656006},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0830451250076294},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.07389816641807556}],"mesh":[{"descriptor_ui":"D000072757","descriptor_name":"Protein Conformation, beta-Strand","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072757","descriptor_name":"Protein Conformation, beta-Strand","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072757","descriptor_name":"Protein Conformation, beta-Strand","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000682","descriptor_name":"Amyloid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000682","descriptor_name":"Amyloid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000682","descriptor_name":"Amyloid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.2c00066","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00066","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:35561002","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35561002","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":[],"awards":[{"id":"https://openalex.org/G1322788651","display_name":null,"funder_award_id":"21977011","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4825017112","display_name":null,"funder_award_id":"GXWD20201231165807007-20200827170132001","funder_id":"https://openalex.org/F4320329791","funder_display_name":"Shenzhen Fundamental Research Program"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320329791","display_name":"Shenzhen Fundamental Research Program","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":87,"referenced_works":["https://openalex.org/W1227630998","https://openalex.org/W1832105192","https://openalex.org/W1893669995","https://openalex.org/W1935356375","https://openalex.org/W1966078827","https://openalex.org/W1977901028","https://openalex.org/W1979371945","https://openalex.org/W1979716756","https://openalex.org/W1986099885","https://openalex.org/W1987754501","https://openalex.org/W1998404472","https://openalex.org/W2007965478","https://openalex.org/W2008146123","https://openalex.org/W2030041905","https://openalex.org/W2040303490","https://openalex.org/W2040809566","https://openalex.org/W2042398225","https://openalex.org/W2043110985","https://openalex.org/W2044750677","https://openalex.org/W2047510784","https://openalex.org/W2049286183","https://openalex.org/W2050333027","https://openalex.org/W2051727755","https://openalex.org/W2051864856","https://openalex.org/W2052316738","https://openalex.org/W2056910212","https://openalex.org/W2064346348","https://openalex.org/W2067258309","https://openalex.org/W2072163112","https://openalex.org/W2076793660","https://openalex.org/W2077042715","https://openalex.org/W2088865014","https://openalex.org/W2108880064","https://openalex.org/W2117537971","https://openalex.org/W2119267663","https://openalex.org/W2132188964","https://openalex.org/W2139229181","https://openalex.org/W2141248208","https://openalex.org/W2142578757","https://openalex.org/W2143264455","https://openalex.org/W2148743566","https://openalex.org/W2155073864","https://openalex.org/W2155143852","https://openalex.org/W2157693914","https://openalex.org/W2164689497","https://openalex.org/W2170665034","https://openalex.org/W2267537819","https://openalex.org/W2312580479","https://openalex.org/W2314944854","https://openalex.org/W2315970507","https://openalex.org/W2327560429","https://openalex.org/W2328874718","https://openalex.org/W2329816046","https://openalex.org/W2333430063","https://openalex.org/W2399137849","https://openalex.org/W2477636673","https://openalex.org/W2511181291","https://openalex.org/W2517316787","https://openalex.org/W2520521682","https://openalex.org/W2532411536","https://openalex.org/W2555870966","https://openalex.org/W2581887313","https://openalex.org/W2736887830","https://openalex.org/W2743441229","https://openalex.org/W2787580408","https://openalex.org/W2790899814","https://openalex.org/W2800697076","https://openalex.org/W2801084441","https://openalex.org/W2802779386","https://openalex.org/W2884157915","https://openalex.org/W2897706713","https://openalex.org/W2910535194","https://openalex.org/W2912172518","https://openalex.org/W2915521488","https://openalex.org/W2922118043","https://openalex.org/W2924014302","https://openalex.org/W2945892680","https://openalex.org/W2963690226","https://openalex.org/W2971913174","https://openalex.org/W2982627636","https://openalex.org/W3000058184","https://openalex.org/W3003589111","https://openalex.org/W3017784424","https://openalex.org/W3103660675","https://openalex.org/W3126049872","https://openalex.org/W3128775947","https://openalex.org/W3197229223"],"related_works":["https://openalex.org/W3127534742","https://openalex.org/W2028501277","https://openalex.org/W2002038078","https://openalex.org/W4366465732","https://openalex.org/W2811043963","https://openalex.org/W2161972019","https://openalex.org/W2312858532","https://openalex.org/W4321013117","https://openalex.org/W2082128336","https://openalex.org/W2295045806"],"abstract_inverted_index":{"Atomic":[0],"descriptions":[1,22],"of":[2,10,17,71,84,128,146,181,202,211,225],"peptide":[3,12,46,188,216],"self-assembly":[4,47,95,127,180,217],"are":[5,40],"crucial":[6],"to":[7,43,65,80,124,214],"an":[8],"understanding":[9],"disease-related":[11,130],"aggregation":[13,60],"and":[14,39,49,78,86,134,148,154,227,241],"the":[15,50,82,119,126,143,156,162,179,196,200,203,209,212,243],"design":[16],"peptide-assembled":[18],"materials.":[19],"Obtaining":[20],"these":[21,247],"through":[23],"computer":[24],"simulation":[25],"is":[26,168,218],"challenging":[27,169],"because":[28],"current":[29],"force":[30,67,96,104,173,204],"fields,":[31],"which":[32,167],"were":[33,76],"not":[34],"designed":[35,77],"for":[36,69,110],"this":[37,90],"process":[38],"often":[41],"unable":[42],"describe":[44],"correctly":[45,193],"behavior":[48],"sequence":[51],"dependence.":[52],"Here,":[53],"we":[54,92],"developed":[55,93,109],"a":[56,62,94,102,165],"framework":[57,236],"using":[58],"dipeptide":[59],"as":[61],"model":[63,215],"system":[64],"improve":[66],"fields":[68],"simulations":[70,141],"self-assembly.":[72],"Aggregation-related":[73],"structural":[74],"properties":[75],"used":[79,123],"guide":[81],"optimization":[83,235],"peptide\u2013peptide":[85,226],"peptide\u2013solvent":[87,228],"interactions.":[88,229,248],"With":[89,113],"framework,":[91],"field,":[97],"termed":[98],"PACE-ASM,":[99],"by":[100,186],"reoptimizing":[101],"hybrid-resolution":[103],"field":[105],"that":[106,208,237],"was":[107,122,231],"originally":[108],"folding":[111,117],"simulation.":[112],"its":[114,222],"applicability":[115],"in":[116,158,245],"simulations,":[118],"new":[120,197],"PACE":[121],"simulate":[125],"two":[129,163],"short":[131],"peptides,":[132],"A\u03b216\u201321":[133,147],"PHF6,":[135],"into":[136],"\u03b2-sheet-rich":[137],"cross-\u03b2":[138,177],"amyloids.":[139],"These":[140],"reproduced":[142],"crystal":[144],"structures":[145],"PHF6":[149],"amyloids":[150,185],"at":[151],"near-atomic":[152],"resolution":[153],"captured":[155],"difference":[157],"packing":[159],"orientations":[160],"between":[161],"sequences,":[164],"task":[166],"even":[170],"with":[171,195,233],"all-atom":[172],"fields.":[174],"Apart":[175],"from":[176],"amyloids,":[178],"emerging":[182],"helix-rich":[183],"cross-\u03b1":[184],"another":[187],"PSM\u03b13":[189],"can":[190,238],"also":[191],"be":[192],"described":[194],"PACE,":[198],"manifesting":[199],"versatility":[201],"field.":[205],"We":[206],"demonstrated":[207],"ability":[210],"PACE-ASM":[213],"based":[219],"largely":[220],"on":[221],"improved":[223],"description":[224],"This":[230],"achieved":[232],"our":[234],"readily":[239],"identify":[240],"address":[242],"deficiency":[244],"describing":[246]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}