{"id":"https://openalex.org/W2965757495","doi":"https://doi.org/10.1021/acs.jcim.9b00426","title":"Autoencoder-Based Detection of Dynamic Allostery Triggered by Ligand Binding Based on Molecular Dynamics","display_name":"Autoencoder-Based Detection of Dynamic Allostery Triggered by Ligand Binding Based on Molecular Dynamics","publication_year":2019,"publication_date":"2019-08-06","ids":{"openalex":"https://openalex.org/W2965757495","doi":"https://doi.org/10.1021/acs.jcim.9b00426","mag":"2965757495","pmid":"https://pubmed.ncbi.nlm.nih.gov/31386362"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00426","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00426","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.9b00426","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":"publisher-specific-oa","license_id":"https://openalex.org/licenses/publisher-specific-oa","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":true,"oa_status":"bronze","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.9b00426","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053746895","display_name":"Yuko Tsuchiya","orcid":"https://orcid.org/0000-0002-7561-4256"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yuko Tsuchiya","raw_affiliation_strings":["Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan"],"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan","institution_ids":["https://openalex.org/I73613424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054344039","display_name":"Kei Taneishi","orcid":"https://orcid.org/0000-0001-8475-5870"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kei Taneishi","raw_affiliation_strings":["Cluster for Science, Technology and Innovation Hub, RIKEN, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan"],"affiliations":[{"raw_affiliation_string":"Cluster for Science, Technology and Innovation Hub, RIKEN, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057742290","display_name":"Yasushige Yonezawa","orcid":"https://orcid.org/0000-0002-7794-7708"},"institutions":[{"id":"https://openalex.org/I916559398","display_name":"Kindai University","ror":"https://ror.org/05kt9ap64","country_code":"JP","type":"education","lineage":["https://openalex.org/I916559398"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasushige Yonezawa","raw_affiliation_strings":["High Pressure Protein Research Center, Institute of Advanced Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan"],"affiliations":[{"raw_affiliation_string":"High Pressure Protein Research Center, Institute of Advanced Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan","institution_ids":["https://openalex.org/I916559398"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5053746895"],"corresponding_institution_ids":["https://openalex.org/I73613424"],"apc_list":null,"apc_paid":null,"fwci":2.2314,"has_fulltext":false,"cited_by_count":48,"citation_normalized_percentile":{"value":0.88729263,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"59","issue":"9","first_page":"4043","last_page":"4051"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.984000027179718,"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"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9807999730110168,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/allosteric-regulation","display_name":"Allosteric regulation","score":0.7953702807426453},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6477113962173462},{"id":"https://openalex.org/keywords/protein-dynamics","display_name":"Protein dynamics","score":0.6437344551086426},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.512239396572113},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.5076178312301636},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4687051475048065},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.45375654101371765},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4300438165664673},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.2026510238647461},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20197933912277222},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.18653473258018494},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.10994303226470947},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.10009849071502686}],"concepts":[{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.7953702807426453},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6477113962173462},{"id":"https://openalex.org/C2775981520","wikidata":"https://www.wikidata.org/wiki/Q17156992","display_name":"Protein dynamics","level":3,"score":0.6437344551086426},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.512239396572113},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.5076178312301636},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4687051475048065},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.45375654101371765},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4300438165664673},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.2026510238647461},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20197933912277222},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.18653473258018494},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.10994303226470947},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.10009849071502686}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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},{"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.9b00426","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00426","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.9b00426","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":"publisher-specific-oa","license_id":"https://openalex.org/licenses/publisher-specific-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:31386362","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31386362","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":{"id":"doi:10.1021/acs.jcim.9b00426","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00426","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.9b00426","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":"publisher-specific-oa","license_id":"https://openalex.org/licenses/publisher-specific-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G345689825","display_name":null,"funder_award_id":"15K07037","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5295307929","display_name":null,"funder_award_id":"JPMJCR14M3","funder_id":"https://openalex.org/F4320338075","funder_display_name":"Core Research for Evolutional Science and Technology"},{"id":"https://openalex.org/G6924707356","display_name":null,"funder_award_id":"17K05620","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7618833572","display_name":null,"funder_award_id":"17K00405","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2965757495.pdf","grobid_xml":"https://content.openalex.org/works/W2965757495.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1964439982","https://openalex.org/W1997167217","https://openalex.org/W2018262140","https://openalex.org/W2022163189","https://openalex.org/W2048183896","https://openalex.org/W2049295438","https://openalex.org/W2072570762","https://openalex.org/W2093174095","https://openalex.org/W2097164795","https://openalex.org/W2108284748","https://openalex.org/W2156839815","https://openalex.org/W2248620004","https://openalex.org/W2283818235","https://openalex.org/W2317028100","https://openalex.org/W2344284775","https://openalex.org/W2417513559","https://openalex.org/W2543720849","https://openalex.org/W2554617421","https://openalex.org/W2744078451","https://openalex.org/W2754595644","https://openalex.org/W2766298563","https://openalex.org/W2780659677","https://openalex.org/W2781487518","https://openalex.org/W2798319431","https://openalex.org/W2800984981","https://openalex.org/W2801476319","https://openalex.org/W2885134480","https://openalex.org/W2886658897","https://openalex.org/W3122822994"],"related_works":["https://openalex.org/W4366407519","https://openalex.org/W2474016806","https://openalex.org/W2073871758","https://openalex.org/W2108284748","https://openalex.org/W2003412353","https://openalex.org/W2010384662","https://openalex.org/W2016704325","https://openalex.org/W2361360078","https://openalex.org/W4390520644","https://openalex.org/W2087585535"],"abstract_inverted_index":{"Dynamic":[0],"allostery":[1],"on":[2,97],"proteins,":[3],"triggered":[4],"by":[5,27,130],"regulator":[6],"binding":[7,15,132],"or":[8,45],"chemical":[9],"modifications,":[10],"transmits":[11],"information":[12],"from":[13,113,157,177],"the":[14,34,38,72,98,107,126,134,139,154,158,174,178,195],"site":[16],"to":[17,51,68,138,184,194],"distant":[18],"regions,":[19],"dramatically":[20],"altering":[21],"protein":[22,55,76,104,203],"function.":[23,56],"It":[24],"is":[25,78,95],"accompanied":[26],"subtle":[28],"changes":[29,39,127],"in":[30,40,106,117,128,133,202],"side-chain":[31],"conformations":[32],"of":[33,54,60,75,100,103,109,141,153,173],"protein,":[35],"indicating":[36],"that":[37,88,125],"dynamics,":[41],"and":[42,62,119,160,198,205],"not":[43],"rigid":[44],"large":[46],"conformational":[47],"changes,":[48],"are":[49],"essential":[50],"understand":[52],"regulation":[53,73],"Although":[57],"a":[58,150,171],"lot":[59],"experimental":[61],"theoretical":[63],"studies":[64],"have":[65],"been":[66],"dedicated":[67],"investigate":[69],"this":[70],"issue,":[71],"mechanism":[74],"function":[77],"still":[79],"being":[80],"debated.":[81],"Here,":[82],"we":[83],"propose":[84],"an":[85],"autoencoder-based":[86,188],"method":[87,94,123,189],"can":[89],"detect":[90],"dynamic":[91,175,185],"allostery.":[92,186],"The":[93],"based":[96],"comparison":[99],"time":[101],"fluctuations":[102],"structures,":[105],"form":[108],"distance":[110],"matrices,":[111],"obtained":[112],"molecular":[114],"dynamics":[115,129],"simulations":[116],"ligand-bound":[118],"-unbound":[120],"forms.":[121],"Our":[122],"detected":[124],"ligand":[131,179],"PDZ2":[135],"domain":[136],"led":[137],"reorganization":[140],"correlative":[142,165],"fluctuation":[143],"motions":[144,156,166],"among":[145],"residue":[146],"pairs,":[147],"which":[148,181],"revealed":[149],"different":[151],"view":[152],"correlated":[155],"PCA":[159],"DCCM.":[161],"In":[162],"addition,":[163],"other":[164],"were":[167],"also":[168],"found":[169],"as":[170],"result":[172],"perturbation":[176],"binding,":[180],"may":[182],"lead":[183],"This":[187],"would":[190],"be":[191],"usefully":[192],"applied":[193],"signal":[196],"transduction":[197],"mutagenesis":[199],"systems":[200],"involved":[201],"functions":[204],"severe":[206],"diseases.":[207]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":6}],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2025-10-10T00:00:00"}