{"id":"https://openalex.org/W2111476716","doi":"https://doi.org/10.1002/(sici)1096-987x(199810)19:13<1534::aid-jcc10>3.0.co;2-i","title":"Multiple time step algorithms for molecular dynamics simulations of proteins: How good are they?","display_name":"Multiple time step algorithms for molecular dynamics simulations of proteins: How good are they?","publication_year":1998,"publication_date":"1998-10-01","ids":{"openalex":"https://openalex.org/W2111476716","doi":"https://doi.org/10.1002/(sici)1096-987x(199810)19:13<1534::aid-jcc10>3.0.co;2-i","mag":"2111476716"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1096-987x(199810)19:13<1534::aid-jcc10>3.0.co;2-i","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(199810)19:13<1534::aid-jcc10>3.0.co;2-i","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/11858/00-001M-0000-000E-CA88-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029685643","display_name":"H. Grubm\ufffdller","orcid":null},"institutions":[{"id":"https://openalex.org/I149899117","display_name":"Max Planck Society","ror":"https://ror.org/01hhn8329","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I149899117"]},{"id":"https://openalex.org/I4210131661","display_name":"Max Planck Institute for Biophysical Chemistry","ror":"https://ror.org/03e76ya46","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210131661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Helmut Grubm\ufffdller","raw_affiliation_strings":["Research Group of Theoretical Molecular Biophysics, MPI for biophysical chemistry, Max Planck Society"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Group of Theoretical Molecular Biophysics, MPI for biophysical chemistry, Max Planck Society","institution_ids":["https://openalex.org/I4210131661","https://openalex.org/I149899117"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042470831","display_name":"Paul Tavan","orcid":null},"institutions":[{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Paul Tavan","raw_affiliation_strings":["Institut fu\u0308r Medizinische Optik, Ludwig\u2013Maximilians-Universita\u0308t Mu\u0308nchen, Oettingenstrasse 67, D-80538 Mu\u0308nchen, Germany","Institut f\u00fcr Medizinische Optik, Ludwig\u2013Maximilians\u2010Universit\u00e4t M\u00fcnchen, Oettingenstrasse 67, D\u201080538 M\u00fcnchen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut fu\u0308r Medizinische Optik, Ludwig\u2013Maximilians-Universita\u0308t Mu\u0308nchen, Oettingenstrasse 67, D-80538 Mu\u0308nchen, Germany","institution_ids":["https://openalex.org/I8204097"]},{"raw_affiliation_string":"Institut f\u00fcr Medizinische Optik, Ludwig\u2013Maximilians\u2010Universit\u00e4t M\u00fcnchen, Oettingenstrasse 67, D\u201080538 M\u00fcnchen, Germany","institution_ids":["https://openalex.org/I8204097"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":1.5501,"has_fulltext":true,"cited_by_count":40,"citation_normalized_percentile":{"value":0.82169319,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"19","issue":"13","first_page":"1534","last_page":"1552"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11177","display_name":"Spectroscopy and Quantum Chemical Studies","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T11177","display_name":"Spectroscopy and Quantum Chemical Studies","score":0.9994999766349792,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9979000091552734,"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.9977999925613403,"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/observable","display_name":"Observable","score":0.7602870464324951},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6363680958747864},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5739190578460693},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5602322220802307},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.5372469425201416},{"id":"https://openalex.org/keywords/trajectory","display_name":"Trajectory","score":0.5356513857841492},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5038716197013855},{"id":"https://openalex.org/keywords/chaotic","display_name":"Chaotic","score":0.5006089210510254},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.44994181394577026},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.43200138211250305},{"id":"https://openalex.org/keywords/cutoff","display_name":"Cutoff","score":0.4271073341369629},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3212123215198517},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1803497076034546},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12653577327728271},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.08194088935852051}],"concepts":[{"id":"https://openalex.org/C32848918","wikidata":"https://www.wikidata.org/wiki/Q845789","display_name":"Observable","level":2,"score":0.7602870464324951},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6363680958747864},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5739190578460693},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5602322220802307},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.5372469425201416},{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.5356513857841492},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5038716197013855},{"id":"https://openalex.org/C2777052490","wikidata":"https://www.wikidata.org/wiki/Q5072826","display_name":"Chaotic","level":2,"score":0.5006089210510254},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.44994181394577026},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.43200138211250305},{"id":"https://openalex.org/C2778217198","wikidata":"https://www.wikidata.org/wiki/Q556977","display_name":"Cutoff","level":2,"score":0.4271073341369629},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3212123215198517},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1803497076034546},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12653577327728271},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.08194088935852051},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1002/(sici)1096-987x(199810)19:13<1534::aid-jcc10>3.0.co;2-i","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(199810)19:13<1534::aid-jcc10>3.0.co;2-i","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},{"id":"pmh:oai:pure.mpg.de:item_1690379","is_oa":true,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-000E-CA88-8","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of computational chemistry","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:pure.mpg.de:item_1690379","is_oa":true,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-000E-CA88-8","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of computational chemistry","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.6100000143051147}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W1558895390","https://openalex.org/W1845480759","https://openalex.org/W1939145901","https://openalex.org/W1968807578","https://openalex.org/W1970747580","https://openalex.org/W1980292953","https://openalex.org/W1980838051","https://openalex.org/W1983702722","https://openalex.org/W1984424792","https://openalex.org/W1985113548","https://openalex.org/W1986966735","https://openalex.org/W1987048011","https://openalex.org/W1989130537","https://openalex.org/W1997716297","https://openalex.org/W1999794194","https://openalex.org/W2003240840","https://openalex.org/W2005386550","https://openalex.org/W2008655335","https://openalex.org/W2011795318","https://openalex.org/W2011842427","https://openalex.org/W2015558782","https://openalex.org/W2015667791","https://openalex.org/W2018415001","https://openalex.org/W2022702839","https://openalex.org/W2025276235","https://openalex.org/W2026498854","https://openalex.org/W2031904472","https://openalex.org/W2032468461","https://openalex.org/W2034852317","https://openalex.org/W2035266068","https://openalex.org/W2035687084","https://openalex.org/W2037424046","https://openalex.org/W2038337607","https://openalex.org/W2038937907","https://openalex.org/W2043672534","https://openalex.org/W2050231602","https://openalex.org/W2057794532","https://openalex.org/W2064150762","https://openalex.org/W2067300234","https://openalex.org/W2068306188","https://openalex.org/W2071740908","https://openalex.org/W2075092972","https://openalex.org/W2077215407","https://openalex.org/W2077562611","https://openalex.org/W2079199763","https://openalex.org/W2080895987","https://openalex.org/W2081540883","https://openalex.org/W2083206954","https://openalex.org/W2083231540","https://openalex.org/W2088294132","https://openalex.org/W2094795801","https://openalex.org/W2100510559","https://openalex.org/W2103636724","https://openalex.org/W2103734924","https://openalex.org/W2105559126","https://openalex.org/W2121432651","https://openalex.org/W2124555222","https://openalex.org/W2135684527","https://openalex.org/W2144897357","https://openalex.org/W2162166182","https://openalex.org/W2170120409","https://openalex.org/W2323178299","https://openalex.org/W2482997221","https://openalex.org/W2761351991","https://openalex.org/W3164510988","https://openalex.org/W4243050008","https://openalex.org/W4299790875"],"related_works":["https://openalex.org/W3092388660","https://openalex.org/W1778838665","https://openalex.org/W1994680671","https://openalex.org/W2002320543","https://openalex.org/W1986953345","https://openalex.org/W2000283393","https://openalex.org/W3175879137","https://openalex.org/W2328322229","https://openalex.org/W2150232912","https://openalex.org/W2119262383"],"abstract_inverted_index":{"We":[0,53],"evaluate":[1],"several":[2],"multiple":[3],"time":[4],"step":[5],"(MTS)":[6],"molecular":[7],"dynamics":[8,18],"(MD)":[9],"methods":[10,104,146],"with":[11,58],"respect":[12,59],"to":[13,22,60,83,133,167],"their":[14,61,110],"suitability":[15],"for":[16,86],"protein":[17,67],"simulations.":[19,52],"In":[20],"contrast":[21],"the":[23,64,70,87,90,113,122,125,143,153],"usual":[24,154],"check":[25],"of":[26,28,33,45,56,66,72,89,92,96,101,112,121,127,136,142,156],"conservation":[27],"total":[29],"energy":[30],"or":[31],"comparisons":[32],"trajectory":[34,79],"details,":[35,80],"we":[36],"chose":[37],"a":[38,43,97],"problem-oriented":[39],"approach":[40],"and":[41,100],"selected":[42],"set":[44],"relevant":[46],"observables":[47,57,123],"computed":[48],"from":[49,149],"extended":[50],"test":[51],"define":[54],"relevance":[55],"role":[62],"in":[63,109,171],"description":[65],"function.":[68],"Accordingly,":[69],"use":[71],"quantities":[73],"that":[74,150,172],"exhibit":[75],"chaotic":[76],"behavior,":[77],"like":[78],"is":[81,105,131,165],"shown":[82,166],"be":[84,168],"inappropriate":[85],"sake":[88],"evaluation":[91],"methods.":[93],"The":[94,139],"accuracy":[95],"cutoff":[98],"method":[99],"six":[102],"MTS":[103],"evaluated,":[106],"which":[107],"differ":[108],"treatment":[111],"computationally":[114],"crucial":[115],"long-ranged":[116],"Coulomb":[117],"interactions.":[118],"For":[119],"each":[120],"considered,":[124],"size":[126],"purely":[128],"statistical":[129],"fluctuations":[130],"determined":[132],"allow":[134],"identification":[135],"algorithmic":[137,157,174],"artifacts.":[138],"obtained":[140,151],"ranking":[141],"considered":[144],"MD":[145],"differs":[147],"significantly":[148],"by":[152],"measures":[155],"accuracy.":[158],"One":[159],"particular":[160],"distance":[161],"class":[162],"method,":[163],"DC-1d,":[164],"clearly":[169],"superior":[170],"no":[173],"artifacts":[175],"were":[176],"detected.":[177],"\u00a9":[178],"1998":[179,190],"John":[180],"Wiley":[181],"&":[182],"Sons,":[183],"Inc.":[184],"J":[185],"Comput":[186],"Chem":[187],"19:":[188],"1534\u20131552,":[189]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-22T06:23:43.705686","created_date":"2025-10-10T00:00:00"}
