{"id":"https://openalex.org/W2529534853","doi":"https://doi.org/10.1063/1.4964776","title":"A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4","display_name":"A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4","publication_year":2016,"publication_date":"2016-10-19","ids":{"openalex":"https://openalex.org/W2529534853","doi":"https://doi.org/10.1063/1.4964776","mag":"2529534853","pmid":"https://pubmed.ncbi.nlm.nih.gov/27782467","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/5074994"},"language":"en","primary_location":{"id":"doi:10.1063/1.4964776","doi":"https://doi.org/10.1063/1.4964776","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.4964776","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["arxiv","crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5074994","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038761014","display_name":"Bradley M. Dickson","orcid":"https://orcid.org/0000-0002-4995-9111","observed_orcids":["https://orcid.org/0000-0002-4995-9111"]},"institutions":[{"id":"https://openalex.org/I1317189400","display_name":"Van Andel Institute","ror":"https://ror.org/00wm07d60","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1317189400"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bradley M. Dickson","raw_affiliation_strings":["Van Andel Research Institute 1 Center for Epigenetics, , 333 Bostwick Avenue, NE, Grand Rapids, Michigan 49503, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Van Andel Research Institute 1 Center for Epigenetics, , 333 Bostwick Avenue, NE, Grand Rapids, Michigan 49503, USA","institution_ids":["https://openalex.org/I1317189400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082863229","display_name":"Parker W. de Waal","orcid":"https://orcid.org/0000-0001-6922-9768","observed_orcids":["https://orcid.org/0000-0001-6922-9768"]},"institutions":[{"id":"https://openalex.org/I1317189400","display_name":"Van Andel Institute","ror":"https://ror.org/00wm07d60","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1317189400"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Parker W. de Waal","raw_affiliation_strings":["Van Andel Research Institute 2 Laboratory of Structural Sciences, , 333 Bostwick Avenue, NE, Grand Rapids, Michigan 49503, USA"],"raw_orcid":"https://orcid.org/0000-0001-6922-9768","affiliations":[{"raw_affiliation_string":"Van Andel Research Institute 2 Laboratory of Structural Sciences, , 333 Bostwick Avenue, NE, Grand Rapids, Michigan 49503, USA","institution_ids":["https://openalex.org/I1317189400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111582551","display_name":"Zachary H. Ramjan","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1317189400","display_name":"Van Andel Institute","ror":"https://ror.org/00wm07d60","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1317189400"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zachary H. Ramjan","raw_affiliation_strings":["Van Andel Research Institute 1 Center for Epigenetics, , 333 Bostwick Avenue, NE, Grand Rapids, Michigan 49503, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Van Andel Research Institute 1 Center for Epigenetics, , 333 Bostwick Avenue, NE, Grand Rapids, Michigan 49503, USA","institution_ids":["https://openalex.org/I1317189400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052217844","display_name":"H. Eric Xu","orcid":"https://orcid.org/0000-0002-6829-8144","observed_orcids":["https://orcid.org/0000-0002-6829-8144"]},"institutions":[{"id":"https://openalex.org/I1317189400","display_name":"Van Andel Institute","ror":"https://ror.org/00wm07d60","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1317189400"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"H. Eric Xu","raw_affiliation_strings":["Shanghai Institute of Materia Medica 3 VARI/SIMM Center, CAS-Key Laboratory of Receptor Research, , Chinese Academy of Sciences, Shanghai 201203, China","Van Andel Research Institute 2 Laboratory of Structural Sciences, , 333 Bostwick Avenue, NE, Grand Rapids, Michigan 49503, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Institute of Materia Medica 3 VARI/SIMM Center, CAS-Key Laboratory of Receptor Research, , Chinese Academy of Sciences, Shanghai 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"raw_affiliation_string":"Van Andel Research Institute 2 Laboratory of Structural Sciences, , 333 Bostwick Avenue, NE, Grand Rapids, Michigan 49503, USA","institution_ids":["https://openalex.org/I1317189400"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004858655","display_name":"Scott B. Rothbart","orcid":"https://orcid.org/0000-0003-1631-5392","observed_orcids":["https://orcid.org/0000-0003-1631-5392"]},"institutions":[{"id":"https://openalex.org/I1317189400","display_name":"Van Andel Institute","ror":"https://ror.org/00wm07d60","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1317189400"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott B. Rothbart","raw_affiliation_strings":["Van Andel Research Institute 1 Center for Epigenetics, , 333 Bostwick Avenue, NE, Grand Rapids, Michigan 49503, USA"],"raw_orcid":"https://orcid.org/0000-0003-1631-5392","affiliations":[{"raw_affiliation_string":"Van Andel Research Institute 1 Center for Epigenetics, , 333 Bostwick Avenue, NE, Grand Rapids, Michigan 49503, USA","institution_ids":["https://openalex.org/I1317189400"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":null,"fwci":2.4366,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.89347094,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"145","issue":"15","first_page":"154113","last_page":"154113"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.7318999767303467,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.7318999767303467,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12534","display_name":"Protein Degradation and Inhibitors","score":0.1949000060558319,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.032600000500679016,"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/free-energy-calculations","display_name":"free energy calculation","score":0.8320000171661377},{"id":"https://openalex.org/keywords/brd4","display_name":"BRD4","score":0.8230000138282776},{"id":"https://openalex.org/keywords/bromodomain-inhibitors","display_name":"bromodomain inhibitors","score":0.9549999833106995},{"id":"https://openalex.org/keywords/ligand-design","display_name":"ligand design","score":0.8999999761581421},{"id":"https://openalex.org/keywords/conformational-switch","display_name":"conformational switching","score":0.8029999732971191},{"id":"https://openalex.org/keywords/binding-free-energy","display_name":"binding free energy","score":0.8679999709129333},{"id":"https://openalex.org/keywords/epigenetic-targets","display_name":"epigenetic targets","score":0.8190000057220459},{"id":"https://openalex.org/keywords/accelerated-molecular-dynamics","display_name":"accelerated molecular dynamics","score":0.7519999742507935},{"id":"https://openalex.org/keywords/open-source-software","display_name":"open source software","score":0.5049999952316284}],"concepts":[{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.8273918032646179},{"id":"https://openalex.org/C6929976","wikidata":"https://www.wikidata.org/wiki/Q3771881","display_name":"Regulator","level":3,"score":0.6828259825706482},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6233549118041992},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.5276759266853333},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5172772407531738},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.48421168327331543},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.457358717918396},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.45442134141921997},{"id":"https://openalex.org/C20254490","wikidata":"https://www.wikidata.org/wiki/Q719550","display_name":"Biasing","level":3,"score":0.4414557218551636},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.42038416862487793},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3508274555206299},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3283695876598358},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.29644399881362915},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.24057629704475403},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19084590673446655},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.18414416909217834},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.1745443046092987},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15942040085792542},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.09649476408958435},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000092468","descriptor_name":"Bromodomain Containing Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D009687","descriptor_name":"Nuclear Proteins","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D009687","descriptor_name":"Nuclear Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016503","descriptor_name":"Drug Delivery Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","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":6,"locations":[{"id":"doi:10.1063/1.4964776","doi":"https://doi.org/10.1063/1.4964776","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.4964776","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:4566925","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5074994","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5074994","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5074994","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"J Chem Phys","raw_type":"Text"},{"id":"pmid:27782467","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27782467","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":"The Journal of chemical physics","raw_type":"Journal Article"},{"id":"pmh:oai:arXiv.org:1609.09833","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1609.09833","pdf_url":"https://arxiv.org/pdf/1609.09833","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.1609.09833","doi":"https://doi.org/10.48550/arxiv.1609.09833","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1609.09833","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:europepmc.org:4566925","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5074994","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1841484166","display_name":"Mechanisms Regulating DNA Methylation Maintenance in Chromatin","funder_award_id":"K99CA181343","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3212207443","display_name":"Mechanisms Regulating DNA Methylation Maintenance in Chromatin","funder_award_id":"R00CA181343","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7401807838","display_name":"Structural Genomics of Orphan Nuclear Receptors","funder_award_id":"R01DK071662","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G932555617","display_name":null,"funder_award_id":"CA181343","funder_id":"https://openalex.org/F4320306080","funder_display_name":"Foundation for the National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306080","display_name":"Foundation for the National Institutes of Health","ror":"https://ror.org/00k86s890"},{"id":"https://openalex.org/F4320308551","display_name":"Van Andel Research Institute","ror":"https://ror.org/00wm07d60"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1965021967","https://openalex.org/W1966078827","https://openalex.org/W1984546455","https://openalex.org/W1989814214","https://openalex.org/W2001996470","https://openalex.org/W2027109368","https://openalex.org/W2028263411","https://openalex.org/W2036537962","https://openalex.org/W2041791898","https://openalex.org/W2049617698","https://openalex.org/W2057806291","https://openalex.org/W2066287229","https://openalex.org/W2103325328","https://openalex.org/W2105391162","https://openalex.org/W2121435438","https://openalex.org/W2124603266","https://openalex.org/W2133620840","https://openalex.org/W2146411229","https://openalex.org/W2146575889","https://openalex.org/W2150981663","https://openalex.org/W2207535250","https://openalex.org/W2233260369","https://openalex.org/W2254627102","https://openalex.org/W2270241120","https://openalex.org/W2270756322","https://openalex.org/W2297831225","https://openalex.org/W2313116527","https://openalex.org/W2316259871"],"related_works":["https://openalex.org/W4221095170","https://openalex.org/W2940408194","https://openalex.org/W3036380204","https://openalex.org/W4394961677","https://openalex.org/W1967482190","https://openalex.org/W2975456198","https://openalex.org/W1967547876","https://openalex.org/W3033947494","https://openalex.org/W3130361983","https://openalex.org/W2618361354"],"abstract_inverted_index":{"In":[0],"this":[1,129],"communication":[2],"we":[3],"introduce":[4],"an":[5,114],"efficient":[6],"implementation":[7,59],"of":[8,16,28,44,73,97,106],"adaptive":[9],"biasing":[10],"that":[11],"greatly":[12],"improves":[13],"the":[14,26,45,86,98],"speed":[15],"free":[17,109],"energy":[18],"computation":[19],"in":[20,85],"molecular":[21],"dynamics":[22],"simulations.":[23],"We":[24],"investigated":[25],"use":[27],"accelerated":[29],"simulations":[30,77],"to":[31,62,101],"inform":[32],"on":[33,53],"compound":[34],"design":[35,117],"using":[36],"a":[37,82,90,102],"recently":[38],"reported":[39],"and":[40,93,119],"clinically":[41],"relevant":[42],"inhibitor":[43,88],"chromatin":[46],"regulator":[47],"BRD4":[48,87],"(bromodomain-containing":[49],"protein":[50],"4).":[51],"Benchmarking":[52],"our":[54,58],"local":[55],"compute":[56],"cluster,":[57],"achieves":[60],"up":[61],"2.5":[63],"times":[64],"more":[65],"force":[66],"calls":[67],"per":[68],"day":[69],"than":[70],"plumed2.":[71],"Results":[72],"five":[74],"1":[75],"\u03bcs-long":[76],"are":[78],"presented,":[79],"which":[80],"reveal":[81],"conformational":[83],"switch":[84,99],"between":[89],"binding":[91,108],"competent":[92],"incompetent":[94],"state.":[95],"Stabilization":[96],"led":[100],"-3":[103],"kcal/mol":[104],"improvement":[105],"absolute":[107],"energy.":[110],"These":[111],"studies":[112],"suggest":[113],"unexplored":[115],"ligand":[116],"principle":[118],"offer":[120],"new":[121],"actionable":[122],"hypotheses":[123],"for":[124],"medicinal":[125],"chemistry":[126],"efforts":[127],"against":[128],"druggable":[130],"epigenetic":[131],"target":[132],"class.":[133]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-10-14T00:00:00"}