{"id":"https://openalex.org/W1997673248","doi":"https://doi.org/10.1063/1.468411","title":"Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation","display_name":"Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation","publication_year":1994,"publication_date":"1994-09-01","ids":{"openalex":"https://openalex.org/W1997673248","doi":"https://doi.org/10.1063/1.468411","mag":"1997673248"},"language":"en","primary_location":{"id":"doi:10.1063/1.468411","doi":"https://doi.org/10.1063/1.468411","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.468411","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref"],"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/A5015956479","display_name":"Minoru Saito","orcid":"https://orcid.org/0000-0002-0249-7773","observed_orcids":["https://orcid.org/0000-0002-0249-7773"]},"institutions":[{"id":"https://openalex.org/I4405284551","display_name":"Protein Engineering Research Institute","ror":"https://ror.org/03s31ff24","country_code":"JP","type":"company","lineage":["https://openalex.org/I4405283708","https://openalex.org/I4405284551"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Minoru Saito","raw_affiliation_strings":["Protein Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Protein Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565, Japan","institution_ids":["https://openalex.org/I4405284551"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5015956479"],"corresponding_institution_ids":["https://openalex.org/I4405284551"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":null,"fwci":2.4038,"has_fulltext":false,"cited_by_count":105,"citation_normalized_percentile":{"value":0.89710038,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"101","issue":"5","first_page":"4055","last_page":"4061"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9951000213623047,"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":0.9951000213623047,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.0044999998062849045,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/long-range-coulomb-interaction","display_name":"long-range Coulomb interaction","score":0.9300000071525574},{"id":"https://openalex.org/keywords/human-lysozyme","display_name":"human lysozyme","score":0.9290000200271606},{"id":"https://openalex.org/keywords/protein-conformational-dynamics","display_name":"protein conformational dynamics","score":0.6759999990463257},{"id":"https://openalex.org/keywords/simulation-artifacts","display_name":"simulation artifacts","score":0.621999979019165},{"id":"https://openalex.org/keywords/charged-residues","display_name":"charged residues","score":0.5979999899864197}],"concepts":[{"id":"https://openalex.org/C2778217198","wikidata":"https://www.wikidata.org/wiki/Q556977","display_name":"Cutoff","level":2,"score":0.9431556463241577},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.8387478590011597},{"id":"https://openalex.org/C9342510","wikidata":"https://www.wikidata.org/wiki/Q25406","display_name":"Coulomb","level":3,"score":0.6391205787658691},{"id":"https://openalex.org/C106195933","wikidata":"https://www.wikidata.org/wiki/Q7847935","display_name":"Truncation (statistics)","level":2,"score":0.597409725189209},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.552280068397522},{"id":"https://openalex.org/C6142545","wikidata":"https://www.wikidata.org/wiki/Q1455881","display_name":"Cutoff frequency","level":2,"score":0.5082961916923523},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.4364531636238098},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.4085189402103424},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.40162503719329834},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.25878503918647766},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.22933709621429443},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.1360945999622345},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.11511245369911194},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09052717685699463},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.06274929642677307},{"id":"https://openalex.org/C147120987","wikidata":"https://www.wikidata.org/wiki/Q2225","display_name":"Electron","level":2,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1063/1.468411","doi":"https://doi.org/10.1063/1.468411","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.468411","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1982425963","https://openalex.org/W1982680156","https://openalex.org/W1992296176","https://openalex.org/W1997630751","https://openalex.org/W2007553441","https://openalex.org/W2010414544","https://openalex.org/W2017164460","https://openalex.org/W2029346657","https://openalex.org/W2041189078","https://openalex.org/W2066757980","https://openalex.org/W2067228077","https://openalex.org/W2079199763","https://openalex.org/W2086741044","https://openalex.org/W2100510559","https://openalex.org/W2110908678","https://openalex.org/W2139741484","https://openalex.org/W2155524113"],"related_works":["https://openalex.org/W4921557","https://openalex.org/W2110908678","https://openalex.org/W2089989244","https://openalex.org/W3092388660","https://openalex.org/W2100510559","https://openalex.org/W1989076564","https://openalex.org/W2046266263","https://openalex.org/W1989349253","https://openalex.org/W2010414544","https://openalex.org/W2063680855"],"abstract_inverted_index":{"Molecular":[0],"dynamics":[1],"(MD)":[2],"simulations":[3,34,62],"of":[4,18,95],"human":[5],"lysozyme":[6],"in":[7,22,118],"water":[8],"were":[9,41,69,84],"carried":[10,42,70],"out":[11,43,71],"for":[12],"400":[13],"ps":[14],"with/without":[15],"the":[16,30,36,58,64,73,81,99,103,107,115,121,125],"truncation":[17],"long-range":[19,37,65],"Coulomb":[20,38,66],"interactions":[21,39,67],"order":[23],"to":[24],"investigate":[25],"artificial":[26],"effects":[27],"caused":[28,89,110],"by":[29,44],"cutoff":[31,76,87,108],"method.":[32,77,105],"MD":[33,61],"with":[35,63,124,130],"included":[40],"using":[45,72],"a":[46,90],"recently":[47],"developed":[48],"method":[49,88,109,127],"[PPPC":[50],"method;":[51],"Mol.":[52],"Simul.":[53],"8,":[54],"321":[55],"(1992)].":[56],"On":[57],"other":[59],"hand,":[60],"truncated":[68],"10":[74],"\u00c5":[75,92],"Comparing":[78],"both":[79],"results,":[80],"following":[82],"artifacts":[83],"found.":[85],"The":[86],"1.7":[91],"larger":[93],"deviation":[94],"charged":[96],"residues":[97],"from":[98,133],"x-ray":[100,134],"structure":[101,117],"than":[102],"PPPC":[104,126],"Further,":[106],"unacceptably":[111],"large":[112],"fluctuation":[113,122],"around":[114],"equilibrium":[116],"water.":[119],"However,":[120],"found":[123],"correlated":[128],"well":[129],"that":[131],"derived":[132],"B-factors.":[135]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":4}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
