{"id":"https://openalex.org/W4310456576","doi":"https://doi.org/10.1021/acs.jcim.2c01173","title":"Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace","display_name":"Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace","publication_year":2022,"publication_date":"2022-11-30","ids":{"openalex":"https://openalex.org/W4310456576","doi":"https://doi.org/10.1021/acs.jcim.2c01173","pmid":"https://pubmed.ncbi.nlm.nih.gov/36449380"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c01173","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01173","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/A5061267883","display_name":"Takunori Yasuda","orcid":"https://orcid.org/0009-0003-9423-0957"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Takunori Yasuda","raw_affiliation_strings":["College of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-0821, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-0821, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054539747","display_name":"Rikuri Morita","orcid":"https://orcid.org/0000-0002-0465-5528"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Rikuri Morita","raw_affiliation_strings":["Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8577, Japan"],"raw_orcid":"https://orcid.org/0000-0002-0465-5528","affiliations":[{"raw_affiliation_string":"Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8577, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048994262","display_name":"Yasuteru Shigeta","orcid":"https://orcid.org/0000-0002-3219-6007"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasuteru Shigeta","raw_affiliation_strings":["Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8577, Japan"],"raw_orcid":"https://orcid.org/0000-0002-3219-6007","affiliations":[{"raw_affiliation_string":"Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8577, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034873036","display_name":"Ryuhei Harada","orcid":"https://orcid.org/0000-0001-7987-0540"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Ryuhei Harada","raw_affiliation_strings":["Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8577, Japan"],"raw_orcid":"https://orcid.org/0000-0001-7987-0540","affiliations":[{"raw_affiliation_string":"Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8577, Japan","institution_ids":["https://openalex.org/I146399215"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5034873036","https://openalex.org/A5061267883"],"corresponding_institution_ids":["https://openalex.org/I146399215"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.12218326,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"62","issue":"23","first_page":"6217","last_page":"6227"},"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":0.998199999332428,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9933000206947327,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"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/subspace-topology","display_name":"Subspace topology","score":0.794575572013855},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.5834043025970459},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5607361197471619},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5101037621498108},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.38261285424232483},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28801417350769043},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.22456172108650208}],"concepts":[{"id":"https://openalex.org/C32834561","wikidata":"https://www.wikidata.org/wiki/Q660730","display_name":"Subspace topology","level":2,"score":0.794575572013855},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.5834043025970459},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5607361197471619},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5101037621498108},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.38261285424232483},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28801417350769043},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.22456172108650208},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.2c01173","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01173","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:36449380","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36449380","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/7","score":0.7699999809265137,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G710677904","display_name":"\u5206\u5b50\u52d5\u529b\u5b66\u8a08\u7b97\u306b\u57fa\u3065\u304f\u30ce\u30f3\u30b3\u30fc\u30c7\u30a3\u30f3\u30b0RNA\u306e\u7acb\u4f53\u69cb\u9020\u4e88\u6e2c","funder_award_id":"22KJ0421","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7151567836","display_name":null,"funder_award_id":"22J20084","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7560602839","display_name":null,"funder_award_id":"JP21K06094","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8113086940","display_name":null,"funder_award_id":"21K06094","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320322832","display_name":"University of Tokyo","ror":"https://ror.org/057zh3y96"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1762595738","https://openalex.org/W1976499671","https://openalex.org/W1976548894","https://openalex.org/W1976904430","https://openalex.org/W1986191025","https://openalex.org/W1987048011","https://openalex.org/W1992899488","https://openalex.org/W1995907662","https://openalex.org/W1998239582","https://openalex.org/W2001398410","https://openalex.org/W2003217171","https://openalex.org/W2008708467","https://openalex.org/W2016033647","https://openalex.org/W2020879467","https://openalex.org/W2025625972","https://openalex.org/W2028263411","https://openalex.org/W2029186981","https://openalex.org/W2034001167","https://openalex.org/W2035687084","https://openalex.org/W2036108598","https://openalex.org/W2039369142","https://openalex.org/W2042821667","https://openalex.org/W2046795100","https://openalex.org/W2048822589","https://openalex.org/W2051994079","https://openalex.org/W2057477511","https://openalex.org/W2057806291","https://openalex.org/W2059551149","https://openalex.org/W2062292777","https://openalex.org/W2063636398","https://openalex.org/W2066951434","https://openalex.org/W2067236515","https://openalex.org/W2069982778","https://openalex.org/W2075460992","https://openalex.org/W2078253946","https://openalex.org/W2079686838","https://openalex.org/W2081693079","https://openalex.org/W2082586732","https://openalex.org/W2084413043","https://openalex.org/W2091513159","https://openalex.org/W2096786184","https://openalex.org/W2103945336","https://openalex.org/W2110507597","https://openalex.org/W2114846189","https://openalex.org/W2126103104","https://openalex.org/W2128572087","https://openalex.org/W2149315921","https://openalex.org/W2149963584","https://openalex.org/W2160723824","https://openalex.org/W2166924299","https://openalex.org/W2179544325","https://openalex.org/W2324726046","https://openalex.org/W2334531949","https://openalex.org/W2334664985","https://openalex.org/W2399447404","https://openalex.org/W2404280981","https://openalex.org/W2463238596","https://openalex.org/W2516776474","https://openalex.org/W2556565974","https://openalex.org/W2560713311","https://openalex.org/W2566432406","https://openalex.org/W2588698822","https://openalex.org/W2754139204","https://openalex.org/W2792512347","https://openalex.org/W2909282192","https://openalex.org/W2910692907","https://openalex.org/W2968426314","https://openalex.org/W3020568877","https://openalex.org/W3048864776","https://openalex.org/W3100801650","https://openalex.org/W3209739359","https://openalex.org/W4283833118"],"related_works":["https://openalex.org/W303980170","https://openalex.org/W2351491280","https://openalex.org/W2386767533","https://openalex.org/W2609315104","https://openalex.org/W2371447506","https://openalex.org/W231025981","https://openalex.org/W2333698505","https://openalex.org/W2129083493","https://openalex.org/W2065107184","https://openalex.org/W2785230770"],"abstract_inverted_index":{"Since":[0],"proteins":[1],"perform":[2],"biological":[3,47],"functions":[4],"through":[5],"their":[6,19,297],"dynamic":[7],"properties,":[8],"molecular":[9],"dynamics":[10],"(MD)":[11],"simulation":[12],"is":[13,42,71,83,92,234],"a":[14,28,32,64,74,95,147,161,229,242,252,277,283,291,331,336],"sophisticated":[15],"strategy":[16],"for":[17,63,146,160,178,276],"investigating":[18],"functions.":[20],"Analyses":[21],"of":[22,39,46,89,190,251,274],"trajectories":[23],"provide":[24],"statistical":[25],"information":[26],"about":[27],"specific":[29],"protein":[30,76,130,254,293,343],"as":[31,77,121,228,237],"free-energy":[33],"landscape":[34],"(FEL).":[35],"However,":[36,80],"the":[37,86,90,122,144,187,204,207,219,247,270,310,320],"timescale":[38],"normal":[40,307],"MD":[41,169],"shorter":[43],"than":[44],"that":[45,266,342],"functions,":[48],"resulting":[49],"in":[50,226,335,347],"statistically":[51],"insufficient":[52],"conformational":[53,272,298,333],"sampling,":[54,155],"finally":[55],"leading":[56],"to":[57,153,176,236,257,290],"unreliable":[58],"FEL":[59],"calculation.":[60],"To":[61,108,215],"search":[62,145,159,177,258,273,299,334],"broad":[65,181,261],"configurational":[66,98,164,182,243,280,339],"subspace,":[67,340],"an":[68,104,115,140,179,259],"external":[69,106,116,124,134],"bias":[70,125,135],"imposed":[72],"on":[73,304],"target":[75],"biased":[78,117,154,351],"sampling.":[79,214],"its":[81],"regulation":[82,118],"challenging":[84],"because":[85,166],"optimal":[87],"strength":[88],"perturbation":[91],"unknown.":[93],"Furthermore,":[94],"physically":[96,148,162,278,337],"irrelevant":[97,163,279],"subspace":[99,165,244],"was":[100,224],"searched":[101],"when":[102],"imposing":[103],"inappropriate":[105],"bias.":[107],"address":[109,216],"this":[110,185,217],"issue,":[111,186,218],"we":[112,201,264],"newly":[113],"proposed":[114],"scheme":[119],"known":[120],"G-factor":[123,205],"limiter":[126],"(GERBIL).":[127],"In":[128,151,327],"GERBIL,":[129],"configurations":[131,191,210],"generated":[132,192,211],"by":[133,139,193,212,245],"are":[136],"structurally":[137],"validated":[138],"indicator":[141],"(G-factor),":[142],"enabling":[143],"relevant":[149,338],"subspace.":[150,183,262,281],"addition":[152],"nonbiased":[156,194,213,230,349],"sampling":[157,195,231,352],"might":[158,268],"repeating":[167],"multiple":[168],"simulations":[170],"from":[171],"several":[172],"initial":[173],"structures":[174],"tends":[175,256],"overly":[180,260],"For":[184],"structural":[188],"qualities":[189,300],"have":[196],"not":[197],"been":[198],"investigated.":[199],"Therefore,":[200],"confirmed":[202],"whether":[203],"screened":[206],"collapsed":[208],"(low-quality)":[209],"outlier":[220,311,321],"flooding":[221],"method":[222],"(OFLOOD)":[223],"adopted":[225],"GERBIL":[227,267],"method,":[232],"which":[233],"referred":[235],"OFLOOD-GERBIL.":[238],"OFLOOD":[239,275,285,308],"rapidly":[240],"expands":[241],"resampling":[246],"rarely":[248],"occurring":[249],"states":[250],"given":[253],"and":[255,286,296,350],"Thus,":[263],"considered":[265],"improve":[269],"excessive":[271],"As":[282],"demonstration,":[284],"OFLOOD-GERBIL":[287,318,329],"were":[288,301],"applied":[289],"globular":[292],"(T4":[294],"lysozyme)":[295],"assessed.":[302],"Based":[303],"our":[305],"assessment,":[306],"without":[309],"validation":[312,322,345],"frequently":[313],"sampled":[314,324],"low-quality":[315],"configurations,":[316],"whereas":[317],"with":[319],"intensively":[323],"high-quality":[325],"configurations.":[326],"conclusion,":[328],"derives":[330],"smart":[332],"indicating":[341],"structure":[344],"works":[346],"both":[348],"methods.":[353]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}
