{"id":"https://openalex.org/W3213031280","doi":"https://doi.org/10.1021/acs.jcim.1c00660","title":"Cryptic Pockets Repository through Pocket Dynamics Tracking and Metadynamics on Essential Dynamics Space: Applications to Mcl-1","display_name":"Cryptic Pockets Repository through Pocket Dynamics Tracking and Metadynamics on Essential Dynamics Space: Applications to Mcl-1","publication_year":2021,"publication_date":"2021-11-08","ids":{"openalex":"https://openalex.org/W3213031280","doi":"https://doi.org/10.1021/acs.jcim.1c00660","mag":"3213031280","pmid":"https://pubmed.ncbi.nlm.nih.gov/34748701"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c00660","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00660","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/A5074249154","display_name":"Mohammed Benabderrahmane","orcid":"https://orcid.org/0000-0002-9515-6942"},"institutions":[{"id":"https://openalex.org/I98702875","display_name":"Universit\u00e9 de Caen Normandie","ror":"https://ror.org/051kpcy16","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I98702875"]},{"id":"https://openalex.org/I4392021217","display_name":"Centre d'Etudes et de Recherche sur le M\u00e9dicament de Normandie","ror":"https://ror.org/012jsqx30","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210105918","https://openalex.org/I4392021217","https://openalex.org/I98702875"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Mohammed Benabderrahmane","raw_affiliation_strings":["Centre d\u2019Etudes et Recherche sur le M\u00e9dicament de Normandie (CERMN), Universit\u00e9 Normandie, UNICAEN, Caen 14000, France"],"affiliations":[{"raw_affiliation_string":"Centre d\u2019Etudes et Recherche sur le M\u00e9dicament de Normandie (CERMN), Universit\u00e9 Normandie, UNICAEN, Caen 14000, France","institution_ids":["https://openalex.org/I98702875","https://openalex.org/I4392021217"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091469186","display_name":"Ronan Bureau","orcid":"https://orcid.org/0000-0001-9404-8117"},"institutions":[{"id":"https://openalex.org/I4392021217","display_name":"Centre d'Etudes et de Recherche sur le M\u00e9dicament de Normandie","ror":"https://ror.org/012jsqx30","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210105918","https://openalex.org/I4392021217","https://openalex.org/I98702875"]},{"id":"https://openalex.org/I98702875","display_name":"Universit\u00e9 de Caen Normandie","ror":"https://ror.org/051kpcy16","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I98702875"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ronan Bureau","raw_affiliation_strings":["Centre d\u2019Etudes et Recherche sur le M\u00e9dicament de Normandie (CERMN), Universit\u00e9 Normandie, UNICAEN, Caen 14000, France"],"affiliations":[{"raw_affiliation_string":"Centre d\u2019Etudes et Recherche sur le M\u00e9dicament de Normandie (CERMN), Universit\u00e9 Normandie, UNICAEN, Caen 14000, France","institution_ids":["https://openalex.org/I98702875","https://openalex.org/I4392021217"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076308838","display_name":"Anne Sophie Voisin\u2010Chiret","orcid":"https://orcid.org/0000-0001-5564-2244"},"institutions":[{"id":"https://openalex.org/I4392021217","display_name":"Centre d'Etudes et de Recherche sur le M\u00e9dicament de Normandie","ror":"https://ror.org/012jsqx30","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210105918","https://openalex.org/I4392021217","https://openalex.org/I98702875"]},{"id":"https://openalex.org/I98702875","display_name":"Universit\u00e9 de Caen Normandie","ror":"https://ror.org/051kpcy16","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I98702875"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Anne Sophie Voisin-Chiret","raw_affiliation_strings":["Centre d\u2019Etudes et Recherche sur le M\u00e9dicament de Normandie (CERMN), Universit\u00e9 Normandie, UNICAEN, Caen 14000, France"],"affiliations":[{"raw_affiliation_string":"Centre d\u2019Etudes et Recherche sur le M\u00e9dicament de Normandie (CERMN), Universit\u00e9 Normandie, UNICAEN, Caen 14000, France","institution_ids":["https://openalex.org/I98702875","https://openalex.org/I4392021217"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079656256","display_name":"Jana Sopkov\u00e1\u2010de Oliveira Santos","orcid":"https://orcid.org/0000-0002-4829-8120"},"institutions":[{"id":"https://openalex.org/I98702875","display_name":"Universit\u00e9 de Caen Normandie","ror":"https://ror.org/051kpcy16","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I98702875"]},{"id":"https://openalex.org/I4392021217","display_name":"Centre d'Etudes et de Recherche sur le M\u00e9dicament de Normandie","ror":"https://ror.org/012jsqx30","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210105918","https://openalex.org/I4392021217","https://openalex.org/I98702875"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Jana Sopkova-de Oliveira Santos","raw_affiliation_strings":["Centre d\u2019Etudes et Recherche sur le M\u00e9dicament de Normandie (CERMN), Universit\u00e9 Normandie, UNICAEN, Caen 14000, France"],"affiliations":[{"raw_affiliation_string":"Centre d\u2019Etudes et Recherche sur le M\u00e9dicament de Normandie (CERMN), Universit\u00e9 Normandie, UNICAEN, Caen 14000, France","institution_ids":["https://openalex.org/I98702875","https://openalex.org/I4392021217"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5079656256"],"corresponding_institution_ids":["https://openalex.org/I4392021217","https://openalex.org/I98702875"],"apc_list":null,"apc_paid":null,"fwci":0.4058,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.60108292,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"61","issue":"11","first_page":"5581","last_page":"5588"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9987999796867371,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9984999895095825,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/metadynamics","display_name":"Metadynamics","score":0.9494364261627197},{"id":"https://openalex.org/keywords/complex-system","display_name":"Complex system","score":0.671488881111145},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6185948252677917},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5598400235176086},{"id":"https://openalex.org/keywords/a-priori-and-a-posteriori","display_name":"A priori and a posteriori","score":0.48198598623275757},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3898738622665405},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35971882939338684},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22562801837921143},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1980210244655609},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16515383124351501},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.13702034950256348}],"concepts":[{"id":"https://openalex.org/C62752575","wikidata":"https://www.wikidata.org/wiki/Q6822487","display_name":"Metadynamics","level":3,"score":0.9494364261627197},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.671488881111145},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6185948252677917},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5598400235176086},{"id":"https://openalex.org/C75553542","wikidata":"https://www.wikidata.org/wiki/Q178161","display_name":"A priori and a posteriori","level":2,"score":0.48198598623275757},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3898738622665405},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35971882939338684},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22562801837921143},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1980210244655609},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16515383124351501},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.13702034950256348},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","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},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.1c00660","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00660","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:34748701","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34748701","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},{"id":"pmh:oai:HAL:hal-03961772v1","is_oa":false,"landing_page_url":"https://hal.science/hal-03961772","pdf_url":null,"source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Chemical Information and Modeling, 2021, 61 (11), pp.5581-5588. &#x27E8;10.1021/acs.jcim.1c00660&#x27E9;","raw_type":"Journal articles"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5830935202","display_name":null,"funder_award_id":"PhD Fellowship to MB","funder_id":"https://openalex.org/F4320322727","funder_display_name":"Minist\u00e8re de l'Education Nationale, de l'Enseignement Superieur et de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320322727","display_name":"Minist\u00e8re de l'Education Nationale, de l'Enseignement Superieur et de la Recherche","ror":"https://ror.org/03sjk9a61"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1972758026","https://openalex.org/W1980067161","https://openalex.org/W1986615462","https://openalex.org/W1993177346","https://openalex.org/W2016370660","https://openalex.org/W2038758364","https://openalex.org/W2040809566","https://openalex.org/W2043558654","https://openalex.org/W2057806291","https://openalex.org/W2060079863","https://openalex.org/W2066951434","https://openalex.org/W2067174909","https://openalex.org/W2070517058","https://openalex.org/W2074160718","https://openalex.org/W2082527753","https://openalex.org/W2109154308","https://openalex.org/W2132589721","https://openalex.org/W2146411229","https://openalex.org/W2150981663","https://openalex.org/W2150996942","https://openalex.org/W2168166668","https://openalex.org/W2177731497","https://openalex.org/W2190199357","https://openalex.org/W2206954826","https://openalex.org/W2292301738","https://openalex.org/W2343614482","https://openalex.org/W2345969009","https://openalex.org/W2520187496","https://openalex.org/W2528270895","https://openalex.org/W2530847795","https://openalex.org/W2783337342","https://openalex.org/W2888970688","https://openalex.org/W2962701388","https://openalex.org/W2990430564","https://openalex.org/W3020865626","https://openalex.org/W3083266070","https://openalex.org/W4241777809"],"related_works":["https://openalex.org/W2599759970","https://openalex.org/W1633592986","https://openalex.org/W1979607105","https://openalex.org/W4385857439","https://openalex.org/W2020879467","https://openalex.org/W4249231514","https://openalex.org/W2964991806","https://openalex.org/W4242006566","https://openalex.org/W1964002518","https://openalex.org/W3131999517"],"abstract_inverted_index":{"Detection":[0],"of":[1,25,81,112,125,131,139,159,196,204,212],"cryptic":[2,26,76,126,150,173,217],"pockets":[3,27,77,218],"(hidden":[4],"protein":[5,52],"pockets)":[6],"is":[7,28,145],"a":[8,49,91,136,169,186,193],"hot":[9],"topic":[10],"in":[11,207,219],"structure-based":[12],"drug":[13],"discovery,":[14],"especially":[15],"for":[16,149,172],"drugging":[17],"the":[18,56,79,95,110,118,123,129,140,157,160,202,209],"yet":[19],"undruggable":[20],"proteome.":[21],"The":[22],"experimental":[23,57],"detection":[24],"still":[29,107],"considered":[30],"an":[31,181,220],"expensive":[32],"endeavor.":[33],"Thus,":[34],"computational":[35],"methods,":[36,86],"such":[37,87,132],"as":[38,88,168,185],"atomistic":[39],"simulations,":[40],"are":[41,106],"used":[42],"instead.":[43],"These":[44],"simulation":[45],"methods":[46,105],"can":[47],"provide":[48,90],"perspective":[50],"on":[51,164],"dynamics":[53,67],"that":[54,144],"overpasses":[55],"X-ray":[58],"structures'":[59],"static":[60],"and":[61,75,215],"average":[62],"view.":[63],"Nonetheless,":[64],"unbiased":[65,100],"molecular":[66],"(MD)":[68],"simulations":[69],"fall":[70],"short":[71],"to":[72,93,116,122,180,191],"detect":[73],"transient":[74],"requiring":[78],"crossing":[80],"high-energy":[82],"barriers.":[83],"Enhanced":[84],"sampling":[85],"Metadynamics,":[89],"solution":[92],"overcome":[94],"time-scale":[96],"problem":[97],"faced":[98],"by":[99,109,146],"MD":[101],"simulations.":[102],"However,":[103],"these":[104],"limited":[108],"availability":[111],"collective":[113,133],"variable":[114],"space":[115,167],"capture":[117],"intricate":[119],"parameters,":[120],"leading":[121],"opening":[124],"pockets.":[127,151],"Unfortunately,":[128],"design":[130],"variables":[134],"requires":[135],"priori":[137],"knowledge":[138],"binding":[141],"site,":[142],"information":[143],"definition":[147],"lacking":[148],"In":[152,189],"this":[153,205],"work,":[154],"we":[155,200],"evaluated":[156],"use":[158],"Metadynamics":[161],"biasing":[162],"scheme":[163],"essential":[165],"coordinates":[166],"general":[170],"method":[171,206],"pocket":[174],"detection.":[175],"This":[176],"approach":[177],"was":[178],"applied":[179],"antiapoptotic":[182],"protein:":[183],"Mcl-1":[184],"test":[187],"model.":[188],"addition":[190],"providing":[192],"broader":[194],"characterization":[195],"Mcl-1's":[197,213],"conformational":[198],"space,":[199],"show":[201],"effectiveness":[203],"drawing":[208],"full":[210],"repository":[211],"known":[214],"novel":[216],"unsupervised":[221],"manner.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-26T15:22:09.906841","created_date":"2025-10-10T00:00:00"}
