{"id":"https://openalex.org/W4406767182","doi":"https://doi.org/10.1021/acs.jcim.4c01981","title":"BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories","display_name":"BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories","publication_year":2025,"publication_date":"2025-01-23","ids":{"openalex":"https://openalex.org/W4406767182","doi":"https://doi.org/10.1021/acs.jcim.4c01981","pmid":"https://pubmed.ncbi.nlm.nih.gov/39846243"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01981","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01981","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/A5083596284","display_name":"Elizaveta Mukhaleva","orcid":"https://orcid.org/0000-0002-9911-7625"},"institutions":[{"id":"https://openalex.org/I4210110459","display_name":"City of Hope","ror":"https://ror.org/01z1vct10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4210110459"]},{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":null,"type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elizaveta Mukhaleva","raw_affiliation_strings":["Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States"],"raw_orcid":"https://orcid.org/0000-0002-9911-7625","affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]},{"raw_affiliation_string":"Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014023048","display_name":"Babgen Manookian","orcid":null},"institutions":[{"id":"https://openalex.org/I4210110459","display_name":"City of Hope","ror":"https://ror.org/01z1vct10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4210110459"]},{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":null,"type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Babgen Manookian","raw_affiliation_strings":["Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101854088","display_name":"Hanyu Chen","orcid":"https://orcid.org/0000-0002-5648-9939"},"institutions":[{"id":"https://openalex.org/I4210110459","display_name":"City of Hope","ror":"https://ror.org/01z1vct10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4210110459"]},{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":null,"type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hanyu Chen","raw_affiliation_strings":["Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]},{"raw_affiliation_string":"Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116008492","display_name":"Indira R. Sivaraj","orcid":null},"institutions":[{"id":"https://openalex.org/I4210110459","display_name":"City of Hope","ror":"https://ror.org/01z1vct10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4210110459"]},{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":null,"type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Indira R. Sivaraj","raw_affiliation_strings":["Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080635161","display_name":"Ning Ma","orcid":"https://orcid.org/0000-0003-4653-7797"},"institutions":[{"id":"https://openalex.org/I4210110459","display_name":"City of Hope","ror":"https://ror.org/01z1vct10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4210110459"]},{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":null,"type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ning Ma","raw_affiliation_strings":["Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States"],"raw_orcid":"https://orcid.org/0000-0003-4653-7797","affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057276803","display_name":"Wenyuan Wei","orcid":"https://orcid.org/0009-0008-5146-8048"},"institutions":[{"id":"https://openalex.org/I4210110459","display_name":"City of Hope","ror":"https://ror.org/01z1vct10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4210110459"]},{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":null,"type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenyuan Wei","raw_affiliation_strings":["Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States"],"raw_orcid":"https://orcid.org/0009-0008-5146-8048","affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]},{"raw_affiliation_string":"Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5098690235","display_name":"Konstancja Urbaniak","orcid":"https://orcid.org/0000-0002-7480-2255"},"institutions":[{"id":"https://openalex.org/I4210110459","display_name":"City of Hope","ror":"https://ror.org/01z1vct10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4210110459"]},{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":null,"type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Konstancja Urbaniak","raw_affiliation_strings":["Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054132482","display_name":"Grigoriy Gogoshin","orcid":"https://orcid.org/0000-0003-0675-1799"},"institutions":[{"id":"https://openalex.org/I4210110459","display_name":"City of Hope","ror":"https://ror.org/01z1vct10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4210110459"]},{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":null,"type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Grigoriy Gogoshin","raw_affiliation_strings":["Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107843977","display_name":"S. Bhattacharya","orcid":"https://orcid.org/0000-0003-0483-2149"},"institutions":[{"id":"https://openalex.org/I4210110459","display_name":"City of Hope","ror":"https://ror.org/01z1vct10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4210110459"]},{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":null,"type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Supriyo Bhattacharya","raw_affiliation_strings":["Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060670368","display_name":"Nagarajan Vaidehi","orcid":"https://orcid.org/0000-0001-8100-8132"},"institutions":[{"id":"https://openalex.org/I4210110459","display_name":"City of Hope","ror":"https://ror.org/01z1vct10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4210110459"]},{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":null,"type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nagarajan Vaidehi","raw_affiliation_strings":["Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States"],"raw_orcid":"https://orcid.org/0000-0001-8100-8132","affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]},{"raw_affiliation_string":"Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041484612","display_name":"Andr\u00e9i S. Rodin","orcid":"https://orcid.org/0000-0002-2570-0332"},"institutions":[{"id":"https://openalex.org/I4210110459","display_name":"City of Hope","ror":"https://ror.org/01z1vct10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4210110459"]},{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":null,"type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andrei S. Rodin","raw_affiliation_strings":["Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]},{"raw_affiliation_string":"Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048043338","display_name":"Sergio Branciamore","orcid":"https://orcid.org/0000-0002-2556-8765"},"institutions":[{"id":"https://openalex.org/I4210110459","display_name":"City of Hope","ror":"https://ror.org/01z1vct10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4210110459"]},{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":null,"type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sergio Branciamore","raw_affiliation_strings":["Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]},{"raw_affiliation_string":"Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States","institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5041484612","https://openalex.org/A5048043338","https://openalex.org/A5060670368","https://openalex.org/A5107843977"],"corresponding_institution_ids":["https://openalex.org/I4210110459","https://openalex.org/I4387156432"],"apc_list":null,"apc_paid":null,"fwci":3.2174,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.91570084,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"65","issue":"3","first_page":"1278","last_page":"1288"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9955999851226807,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9951000213623047,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5635236501693726},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4979686737060547},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.48760905861854553},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.48396065831184387},{"id":"https://openalex.org/keywords/bayesian-network","display_name":"Bayesian network","score":0.4808507561683655},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33153218030929565},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1968032717704773},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12959256768226624},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.10551464557647705}],"concepts":[{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5635236501693726},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4979686737060547},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.48760905861854553},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.48396065831184387},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.4808507561683655},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33153218030929565},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1968032717704773},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12959256768226624},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.10551464557647705},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":2,"locations":[{"id":"doi:10.1021/acs.jcim.4c01981","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01981","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:39846243","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39846243","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":[],"awards":[{"id":"https://openalex.org/G1287643243","display_name":null,"funder_award_id":"R01-GM117923","funder_id":"https://openalex.org/F5606758034","funder_display_name":"All of Us Research Program"},{"id":"https://openalex.org/G5359993054","display_name":null,"funder_award_id":"R01- LM013876","funder_id":"https://openalex.org/F5606758034","funder_display_name":"All of Us Research Program"},{"id":"https://openalex.org/G6412235000","display_name":null,"funder_award_id":"R01-LM013138","funder_id":"https://openalex.org/F5606758034","funder_display_name":"All of Us Research Program"}],"funders":[{"id":"https://openalex.org/F5606758034","display_name":"All of Us Research Program","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1674510714","https://openalex.org/W1886386345","https://openalex.org/W1980073965","https://openalex.org/W1980857039","https://openalex.org/W1981122373","https://openalex.org/W1999957860","https://openalex.org/W2011168681","https://openalex.org/W2021520922","https://openalex.org/W2027280942","https://openalex.org/W2036108598","https://openalex.org/W2036919909","https://openalex.org/W2042934054","https://openalex.org/W2067174909","https://openalex.org/W2072899780","https://openalex.org/W2074452851","https://openalex.org/W2075955627","https://openalex.org/W2078876572","https://openalex.org/W2081693079","https://openalex.org/W2092417121","https://openalex.org/W2098055048","https://openalex.org/W2110585820","https://openalex.org/W2118233996","https://openalex.org/W2121146753","https://openalex.org/W2121278567","https://openalex.org/W2132262459","https://openalex.org/W2140831051","https://openalex.org/W2141960720","https://openalex.org/W2142635246","https://openalex.org/W2144391203","https://openalex.org/W2150981663","https://openalex.org/W2159675211","https://openalex.org/W2160544821","https://openalex.org/W2168175751","https://openalex.org/W2168269595","https://openalex.org/W2170711116","https://openalex.org/W2283818235","https://openalex.org/W2319505095","https://openalex.org/W2336171845","https://openalex.org/W2395425574","https://openalex.org/W2510475640","https://openalex.org/W2524991337","https://openalex.org/W2555870966","https://openalex.org/W2604971487","https://openalex.org/W2765372792","https://openalex.org/W2790984926","https://openalex.org/W2791604663","https://openalex.org/W2803284534","https://openalex.org/W2889733245","https://openalex.org/W2927778654","https://openalex.org/W2944371911","https://openalex.org/W2946614862","https://openalex.org/W2978449141","https://openalex.org/W2987740792","https://openalex.org/W2996405687","https://openalex.org/W3089969599","https://openalex.org/W3099423575","https://openalex.org/W3118749273","https://openalex.org/W3150506609","https://openalex.org/W3164232678","https://openalex.org/W4231415818","https://openalex.org/W4239632189","https://openalex.org/W4293729999","https://openalex.org/W4312045153","https://openalex.org/W4384068486","https://openalex.org/W4385654875","https://openalex.org/W4390520644","https://openalex.org/W4390807140","https://openalex.org/W4393088399","https://openalex.org/W4396807266","https://openalex.org/W4402718494","https://openalex.org/W4403460892","https://openalex.org/W4405080689"],"related_works":["https://openalex.org/W2023156907","https://openalex.org/W3094899115","https://openalex.org/W1968806281","https://openalex.org/W3095515585","https://openalex.org/W2972991241","https://openalex.org/W4315498887","https://openalex.org/W4378377190","https://openalex.org/W4401585471","https://openalex.org/W2360970307","https://openalex.org/W1773535258"],"abstract_inverted_index":{"Bayesian":[0],"network":[1,167],"modeling":[2],"(BN":[3],"modeling,":[4],"or":[5],"BNM)":[6],"is":[7,147],"an":[8,205],"interpretable":[9],"machine":[10],"learning":[11],"method":[12],"for":[13,92,158,198,236],"constructing":[14],"probabilistic":[15,165],"graphical":[16,166],"models":[17,103],"from":[18],"the":[19,56,70,75,79,84,94,110,114,127,133,138,148,172,175,186,202,222],"data.":[20,142],"In":[21,122],"recent":[22],"years,":[23],"it":[24],"has":[25,52,62],"been":[26,64],"extensively":[27],"applied":[28],"to":[29,39,137,152,185,200,216,228],"diverse":[30],"types":[31],"of":[32,58,74,83,97,113,240],"biomedical":[33],"data":[34],"sets.":[35],"Concurrently,":[36],"our":[37],"ability":[38],"perform":[40],"long-time":[41],"scale":[42],"molecular":[43],"dynamics":[44],"(MD)":[45],"simulations":[46],"on":[47,69],"proteins":[48],"and":[49,81,155,180,195,213],"other":[50],"materials":[51],"increased":[53],"exponentially.":[54],"However,":[55],"analysis":[57],"MD":[59,85,95,139,160,238],"simulation":[60,140,161],"trajectories":[61,96,141,162,239],"not":[63],"data-driven":[65,107],"but":[66],"rather":[67],"dependent":[68],"user's":[71],"prior":[72],"knowledge":[73],"systems,":[76],"thus":[77],"limiting":[78],"scope":[80],"utility":[82],"simulations.":[86],"Recently,":[87],"we":[88,125,208],"pioneered":[89],"using":[90,163],"BNM":[91,134,189],"analyzing":[93,159,237],"protein":[98,242],"complexes.":[99],"The":[100,231],"resulting":[101],"BN":[102],"yield":[104],"novel":[105],"fully":[106],"insights":[108],"into":[109],"functional":[111],"importance":[112],"amino":[115],"acid":[116],"residues":[117],"that":[118,131,145],"modulate":[119],"proteins'":[120],"function.":[121],"this":[123,211],"report,":[124],"describe":[126,170],"BaNDyT":[128,146],"software":[129,150,215,232],"package":[130,151],"implements":[132],"specifically":[135,221],"attuned":[136],"We":[143,169],"believe":[144],"first":[149],"include":[153],"specialized":[154],"advanced":[156],"features":[157],"a":[164,181,193],"model.":[168],"here":[171],"software's":[173],"uses,":[174],"methods":[176],"associated":[177,214],"with":[178],"it,":[179],"comprehensive":[182],"Python":[183],"interface":[184],"underlying":[187],"generalist":[188],"code.":[190],"This":[191],"provides":[192],"powerful":[194],"versatile":[196],"mechanism":[197],"users":[199],"control":[201],"workflow.":[203],"As":[204],"application":[206],"example,":[207],"have":[209],"utilized":[210],"methodology":[212],"study":[217],"how":[218],"membrane":[219],"proteins,":[220],"G":[223,229],"protein-coupled":[224],"receptors,":[225],"selectively":[226],"couple":[227],"proteins.":[230],"can":[233],"be":[234],"used":[235],"any":[241],"as":[243,245],"well":[244],"polymeric":[246],"materials.":[247]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5}],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2025-10-10T00:00:00"}