{"id":"https://openalex.org/W2131377322","doi":"https://doi.org/10.1002/prot.22841","title":"Large\u2010scale comparison of protein essential dynamics from molecular dynamics simulations and coarse\u2010grained normal mode analyses","display_name":"Large\u2010scale comparison of protein essential dynamics from molecular dynamics simulations and coarse\u2010grained normal mode analyses","publication_year":2010,"publication_date":"2010-08-15","ids":{"openalex":"https://openalex.org/W2131377322","doi":"https://doi.org/10.1002/prot.22841","mag":"2131377322","pmid":"https://pubmed.ncbi.nlm.nih.gov/20848551"},"language":"en","primary_location":{"id":"doi:10.1002/prot.22841","doi":"https://doi.org/10.1002/prot.22841","is_oa":false,"landing_page_url":"https://doi.org/10.1002/prot.22841","pdf_url":null,"source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"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":"Proteins: Structure, Function, and Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"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/A5023026000","display_name":"Aqeel Ahmed","orcid":"https://orcid.org/0000-0002-2907-2433","observed_orcids":["https://orcid.org/0000-0002-2907-2433"]},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]},{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Aqeel Ahmed","raw_affiliation_strings":["Department of Biological Sciences, Molecular Bioinformatics Group, Goethe-University, Frankfurt, Germany","Current address: Department of Biochemistry & Molecular Biophysics, The University of Arizona, Tucson, Arizona"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Molecular Bioinformatics Group, Goethe-University, Frankfurt, Germany","institution_ids":["https://openalex.org/I114090438"]},{"raw_affiliation_string":"Current address: Department of Biochemistry & Molecular Biophysics, The University of Arizona, Tucson, Arizona","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064728810","display_name":"Saskia Villinger","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]},{"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","https://openalex.org/I4387154714"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Saskia Villinger","raw_affiliation_strings":["Current address: Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Go\u0308ttingen, Germany","Department of Biological Sciences, Molecular Bioinformatics Group, Goethe-University, Frankfurt, Germany","Current address: Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, G\u00f6ttingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Current address: Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Go\u0308ttingen, Germany","institution_ids":["https://openalex.org/I4210131661"]},{"raw_affiliation_string":"Department of Biological Sciences, Molecular Bioinformatics Group, Goethe-University, Frankfurt, Germany","institution_ids":["https://openalex.org/I114090438"]},{"raw_affiliation_string":"Current address: Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I4210131661"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063949219","display_name":"Holger Gohlke","orcid":"https://orcid.org/0000-0001-8613-1447","observed_orcids":["https://orcid.org/0000-0001-8613-1447"]},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]},{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Holger Gohlke","raw_affiliation_strings":["Department of Biological Sciences, Molecular Bioinformatics Group, Goethe-University, Frankfurt, Germany","Department of Mathematics and Natural Sciences, Heinrich-Heine-University, Du\u0308sseldorf, Germany","Department of Mathematics and Natural Sciences, Heinrich-Heine-University, D\u00fcsseldorf, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Molecular Bioinformatics Group, Goethe-University, Frankfurt, Germany","institution_ids":["https://openalex.org/I114090438"]},{"raw_affiliation_string":"Department of Mathematics and Natural Sciences, Heinrich-Heine-University, Du\u0308sseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Department of Mathematics and Natural Sciences, Heinrich-Heine-University, D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5063949219"],"corresponding_institution_ids":["https://openalex.org/I114090438","https://openalex.org/I44260953"],"apc_list":{"value":4550,"currency":"USD","value_usd":4550},"apc_paid":null,"fwci":1.9115,"has_fulltext":false,"cited_by_count":48,"citation_normalized_percentile":{"value":0.85725341,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"78","issue":"16","first_page":"3341","last_page":"3352"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":1.0,"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":1.0,"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":0.0,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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":0.0,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/elastic-network-model","display_name":"elastic network model","score":0.996999979019165},{"id":"https://openalex.org/keywords/low-frequency-normal-modes","display_name":"low-frequency normal modes","score":0.8159999847412109},{"id":"https://openalex.org/keywords/vibrational-dynamics","display_name":"vibrational dynamics","score":0.5289999842643738}],"concepts":[{"id":"https://openalex.org/C32758168","wikidata":"https://www.wikidata.org/wiki/Q900488","display_name":"Normal mode","level":3,"score":0.8118374943733215},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.6279327273368835},{"id":"https://openalex.org/C2775981520","wikidata":"https://www.wikidata.org/wiki/Q17156992","display_name":"Protein dynamics","level":3,"score":0.578453779220581},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5754438042640686},{"id":"https://openalex.org/C48677424","wikidata":"https://www.wikidata.org/wiki/Q6888088","display_name":"Mode (computer interface)","level":2,"score":0.5407403111457825},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5297884345054626},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5047451257705688},{"id":"https://openalex.org/C177774035","wikidata":"https://www.wikidata.org/wiki/Q1246948","display_name":"Granularity","level":2,"score":0.4972386658191681},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.4592454731464386},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.44816210865974426},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.4413783550262451},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.346910685300827},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26955369114875793},{"id":"https://openalex.org/C198394728","wikidata":"https://www.wikidata.org/wiki/Q3695508","display_name":"Vibration","level":2,"score":0.12008979916572571},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0914105474948883},{"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009038","descriptor_name":"Motion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":true}],"locations_count":3,"locations":[{"id":"doi:10.1002/prot.22841","doi":"https://doi.org/10.1002/prot.22841","is_oa":false,"landing_page_url":"https://doi.org/10.1002/prot.22841","pdf_url":null,"source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"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":"Proteins: Structure, Function, and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20848551","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20848551","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,"listed_in":[],"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":"Proteins","raw_type":"Comparative Study"},{"id":"mag:2189464758","doi":null,"is_oa":false,"landing_page_url":"http://www.cpclab.uni-duesseldorf.de/publications/publications/53.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":101,"referenced_works":["https://openalex.org/W149879337","https://openalex.org/W409604127","https://openalex.org/W1966041739","https://openalex.org/W1968407616","https://openalex.org/W1969875513","https://openalex.org/W1972244704","https://openalex.org/W1972317081","https://openalex.org/W1973834037","https://openalex.org/W1977630495","https://openalex.org/W1977729499","https://openalex.org/W1977782382","https://openalex.org/W1978159078","https://openalex.org/W1989161865","https://openalex.org/W1992945955","https://openalex.org/W1996765646","https://openalex.org/W1997486650","https://openalex.org/W1998122941","https://openalex.org/W1998412941","https://openalex.org/W2001208576","https://openalex.org/W2001753219","https://openalex.org/W2002001977","https://openalex.org/W2004067483","https://openalex.org/W2013643300","https://openalex.org/W2013901674","https://openalex.org/W2019683054","https://openalex.org/W2021419438","https://openalex.org/W2022488335","https://openalex.org/W2025088751","https://openalex.org/W2031340110","https://openalex.org/W2032372720","https://openalex.org/W2037760012","https://openalex.org/W2039425860","https://openalex.org/W2041578033","https://openalex.org/W2046408940","https://openalex.org/W2047346757","https://openalex.org/W2048287651","https://openalex.org/W2049598343","https://openalex.org/W2049888624","https://openalex.org/W2049961618","https://openalex.org/W2051893115","https://openalex.org/W2052085704","https://openalex.org/W2052329232","https://openalex.org/W2053999477","https://openalex.org/W2055395721","https://openalex.org/W2055956723","https://openalex.org/W2056331547","https://openalex.org/W2057400263","https://openalex.org/W2060665868","https://openalex.org/W2063962473","https://openalex.org/W2067337097","https://openalex.org/W2067763399","https://openalex.org/W2068128475","https://openalex.org/W2069777230","https://openalex.org/W2069920107","https://openalex.org/W2070825039","https://openalex.org/W2079199763","https://openalex.org/W2084267038","https://openalex.org/W2084406464","https://openalex.org/W2085227451","https://openalex.org/W2086385790","https://openalex.org/W2086871476","https://openalex.org/W2088906583","https://openalex.org/W2093547815","https://openalex.org/W2093634504","https://openalex.org/W2101017457","https://openalex.org/W2102449622","https://openalex.org/W2103212553","https://openalex.org/W2103420861","https://openalex.org/W2105175831","https://openalex.org/W2105438341","https://openalex.org/W2106988671","https://openalex.org/W2107238748","https://openalex.org/W2108067237","https://openalex.org/W2110473722","https://openalex.org/W2113030357","https://openalex.org/W2113994268","https://openalex.org/W2114876189","https://openalex.org/W2115928493","https://openalex.org/W2118542302","https://openalex.org/W2123035826","https://openalex.org/W2123529526","https://openalex.org/W2125213515","https://openalex.org/W2126551164","https://openalex.org/W2130541969","https://openalex.org/W2132589721","https://openalex.org/W2134742468","https://openalex.org/W2139176856","https://openalex.org/W2140889378","https://openalex.org/W2141184730","https://openalex.org/W2149301682","https://openalex.org/W2149744037","https://openalex.org/W2152193893","https://openalex.org/W2152997134","https://openalex.org/W2156115459","https://openalex.org/W2156350373","https://openalex.org/W2159409289","https://openalex.org/W2160294964","https://openalex.org/W2164804788","https://openalex.org/W2168172687","https://openalex.org/W2939287563","https://openalex.org/W3145607791"],"related_works":["https://openalex.org/W2189464758","https://openalex.org/W6981123317","https://openalex.org/W2002001977","https://openalex.org/W7101214697","https://openalex.org/W1983353234","https://openalex.org/W2064068263","https://openalex.org/W2084631697","https://openalex.org/W4302065803","https://openalex.org/W2223938323","https://openalex.org/W2308610496"],"abstract_inverted_index":{"A":[0],"large-scale":[1],"comparison":[2],"of":[3,26,60,62,67,86,98,103,135,142,168,178,184,199,206,215,217],"essential":[4],"dynamics":[5,202],"(ED)":[6],"modes":[7,14,49,57,77,100,120,152],"from":[8,15,50,78],"molecular":[9],"dynamic":[10],"simulations":[11],"and":[12,37,64,118],"normal":[13,17,41,48,76],"coarse-grained":[16],"mode":[18,42],"methods":[19],"(CGNM)":[20],"was":[21,73],"performed":[22],"on":[23],"a":[24,70,83,207],"dataset":[25],"335":[27],"proteins.":[28],"As":[29],"CGNM":[30,119,136,151],"methods,":[31],"the":[32,38,91,95,104,108,132,163,169,200,218],"elastic":[33],"network":[34],"model":[35],"(ENM)":[36],"rigid":[39],"cluster":[40],"analysis":[43],"(RCNMA)":[44],"were":[45,80,128,153],"used.":[46],"Low-frequency":[47],"ENM":[51,99],"correlate":[52],"very":[53],"well":[54],"with":[55,144],"ED":[56,110,117,174,190],"in":[58,192],"terms":[59],"directions":[61],"motions":[63,141],"relative":[65],"amplitudes":[66],"motions.":[68],"Notably,":[69],"similar":[71],"performance":[72],"found":[74,154],"if":[75],"RCNMA":[79],"used,":[81],"despite":[82],"higher":[84],"level":[85],"coarse":[87],"graining.":[88],"On":[89],"average,":[90],"space":[92,105],"spanned":[93,106],"by":[94,107,221],"first":[96],"quarter":[97],"describes":[101],"84%":[102],"five":[109],"modes.":[111,175],"Furthermore,":[112],"no":[113],"prominent":[114],"differences":[115],"for":[116,138],"among":[121,159],"different":[122],"protein":[123],"structure":[124],"classes":[125],"(CATH":[126],"classification)":[127],"found.":[129],"This":[130],"demonstrates":[131],"general":[133],"potential":[134],"approaches":[137],"describing":[139],"intrinsic":[140],"proteins":[143,160],"little":[145],"computational":[146],"cost.":[147],"For":[148],"selected":[149],"cases,":[150,194],"to":[155,212],"be":[156,197],"more":[157],"robust":[158],"that":[161,189,203],"have":[162],"same":[164,170],"topology":[165],"or":[166],"are":[167,204],"homologous":[171],"superfamily":[172],"than":[173],"In":[176],"view":[177],"recent":[179],"evidence":[180],"regarding":[181],"evolutionary":[182],"conservation":[183],"vibrational":[185],"dynamics,":[186],"this":[187],"suggests":[188],"modes,":[191],"some":[193,216],"might":[195],"not":[196],"representative":[198],"underlying":[201],"characteristic":[205],"whole":[208],"family,":[209],"probably":[210],"due":[211],"insufficient":[213],"sampling":[214],"family":[219],"members":[220],"MD.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":8}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}