{"id":"https://openalex.org/W4399916751","doi":"https://doi.org/10.1021/acs.jcim.3c02007","title":"MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search","display_name":"MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search","publication_year":2024,"publication_date":"2024-06-22","ids":{"openalex":"https://openalex.org/W4399916751","doi":"https://doi.org/10.1021/acs.jcim.3c02007","pmid":"https://pubmed.ncbi.nlm.nih.gov/38907694"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c02007","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c02007","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c02007","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c02007","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045119527","display_name":"Zakaria Larbi Dahmani","orcid":"https://orcid.org/0009-0005-8002-3169"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I4210145605","display_name":"Institut de min\u00e9ralogie, de physique des mat\u00e9riaux et de cosmochimie","ror":"https://ror.org/05abgg682","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I39804081","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210098836","https://openalex.org/I4210113730","https://openalex.org/I4210123595","https://openalex.org/I4210131494","https://openalex.org/I4210145605","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR","US"],"is_corresponding":false,"raw_author_name":"Zakaria L. Dahmani","raw_affiliation_strings":["School of Medicine, Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch I Bldg, 3420 Forbes Avenue, Pittsburgh, Pennsylvania 15260, United States","UMR 7590, CNRS, Museum National d\u2019Histoire Naturelle, Institut de Min\u00e9ralogie, Physique des Mat\u00e9riaux et Cosmochimie, IMPMC, Sorbonne Universit\u00e9, 4 place Jussieu, Paris 75005, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medicine, Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch I Bldg, 3420 Forbes Avenue, Pittsburgh, Pennsylvania 15260, United States","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"UMR 7590, CNRS, Museum National d\u2019Histoire Naturelle, Institut de Min\u00e9ralogie, Physique des Mat\u00e9riaux et Cosmochimie, IMPMC, Sorbonne Universit\u00e9, 4 place Jussieu, Paris 75005, France","institution_ids":["https://openalex.org/I39804081","https://openalex.org/I4210145605","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048255926","display_name":"Ana L\u00edgia Scott","orcid":"https://orcid.org/0000-0002-8053-1834"},"institutions":[{"id":"https://openalex.org/I4210086872","display_name":"Institut de g\u00e9n\u00e9tique et de biologie mol\u00e9culaire et cellulaire","ror":"https://ror.org/0015ws592","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I4210086872","https://openalex.org/I4210096427","https://openalex.org/I68947357"]},{"id":"https://openalex.org/I68947357","display_name":"Universit\u00e9 de Strasbourg","ror":"https://ror.org/00pg6eq24","country_code":"FR","type":"education","lineage":["https://openalex.org/I68947357"]},{"id":"https://openalex.org/I71715416","display_name":"Universidade Federal do ABC","ror":"https://ror.org/028kg9j04","country_code":"BR","type":"education","lineage":["https://openalex.org/I71715416"]}],"countries":["BR","FR"],"is_corresponding":false,"raw_author_name":"Ana Ligia Scott","raw_affiliation_strings":["CMCC, Computational Biophysics and Biology, Universidade Federal do ABC, Avenida dos Estados 5001, S\u00e3o Paulo, Santo Andr\u00e9 09210-580, Brazil","Universit\u00e9 de Strasbourg\u2500IGBMC\u2500Departament de Biologie structurale integrative, 1 rue Laurent Fries BP, Illkirch 10142 67404, CEDEX, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CMCC, Computational Biophysics and Biology, Universidade Federal do ABC, Avenida dos Estados 5001, S\u00e3o Paulo, Santo Andr\u00e9 09210-580, Brazil","institution_ids":["https://openalex.org/I71715416"]},{"raw_affiliation_string":"Universit\u00e9 de Strasbourg\u2500IGBMC\u2500Departament de Biologie structurale integrative, 1 rue Laurent Fries BP, Illkirch 10142 67404, CEDEX, France","institution_ids":["https://openalex.org/I68947357","https://openalex.org/I4210086872"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050836858","display_name":"Catherine V\u00e9nien\u2010Bryan","orcid":"https://orcid.org/0000-0002-7328-3764"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I4210145605","display_name":"Institut de min\u00e9ralogie, de physique des mat\u00e9riaux et de cosmochimie","ror":"https://ror.org/05abgg682","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I39804081","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210098836","https://openalex.org/I4210113730","https://openalex.org/I4210123595","https://openalex.org/I4210131494","https://openalex.org/I4210145605","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Catherine V\u00e9nien-Bryan","raw_affiliation_strings":["UMR 7590, CNRS, Museum National d\u2019Histoire Naturelle, Institut de Min\u00e9ralogie, Physique des Mat\u00e9riaux et Cosmochimie, IMPMC, Sorbonne Universit\u00e9, 4 place Jussieu, Paris 75005, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UMR 7590, CNRS, Museum National d\u2019Histoire Naturelle, Institut de Min\u00e9ralogie, Physique des Mat\u00e9riaux et Cosmochimie, IMPMC, Sorbonne Universit\u00e9, 4 place Jussieu, Paris 75005, France","institution_ids":["https://openalex.org/I39804081","https://openalex.org/I4210145605","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043151942","display_name":"David P\u00e9rahia","orcid":"https://orcid.org/0000-0001-7480-3349"},"institutions":[{"id":"https://openalex.org/I11559806","display_name":"\u00c9cole Normale Sup\u00e9rieure Paris-Saclay","ror":"https://ror.org/00hx6zz33","country_code":"FR","type":"education","lineage":["https://openalex.org/I11559806","https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210150317","display_name":"Laboratoire de Biologie et Pharmacologie Appliqu\u00e9e","ror":"https://ror.org/03njrcx45","country_code":"FR","type":"facility","lineage":["https://openalex.org/I11559806","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I277688954","https://openalex.org/I4210096427","https://openalex.org/I4210150317"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"David Perahia","raw_affiliation_strings":["Laboratoire de Biologie et Pharmacologie Appliqu\u00e9e, UMR 8113, \u00c9cole Normale Sup\u00e9rieure Paris-Saclay, Gif-sur-Yvette 91190, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire de Biologie et Pharmacologie Appliqu\u00e9e, UMR 8113, \u00c9cole Normale Sup\u00e9rieure Paris-Saclay, Gif-sur-Yvette 91190, France","institution_ids":["https://openalex.org/I4210150317","https://openalex.org/I11559806"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031703110","display_name":"Maur\u00edcio G. S. Costa","orcid":"https://orcid.org/0000-0001-5443-286X"},"institutions":[{"id":"https://openalex.org/I11559806","display_name":"\u00c9cole Normale Sup\u00e9rieure Paris-Saclay","ror":"https://ror.org/00hx6zz33","country_code":"FR","type":"education","lineage":["https://openalex.org/I11559806","https://openalex.org/I277688954"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I4210145605","display_name":"Institut de min\u00e9ralogie, de physique des mat\u00e9riaux et de cosmochimie","ror":"https://ror.org/05abgg682","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I39804081","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210098836","https://openalex.org/I4210113730","https://openalex.org/I4210123595","https://openalex.org/I4210131494","https://openalex.org/I4210145605","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210150317","display_name":"Laboratoire de Biologie et Pharmacologie Appliqu\u00e9e","ror":"https://ror.org/03njrcx45","country_code":"FR","type":"facility","lineage":["https://openalex.org/I11559806","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I277688954","https://openalex.org/I4210096427","https://openalex.org/I4210150317"]},{"id":"https://openalex.org/I52325","display_name":"Funda\u00e7\u00e3o Oswaldo Cruz","ror":"https://ror.org/04jhswv08","country_code":"BR","type":"facility","lineage":["https://openalex.org/I52325"]}],"countries":["BR","FR"],"is_corresponding":true,"raw_author_name":"Mauricio G.S Costa","raw_affiliation_strings":["Laboratoire de Biologie et Pharmacologie Appliqu\u00e9e, UMR 8113, \u00c9cole Normale Sup\u00e9rieure Paris-Saclay, Gif-sur-Yvette 91190, France","Programa de Computa\u00e7\u00e3o Cient\u00edfica, Vice-Presid\u00eancia de Educa\u00e7\u00e3o, Informa\u00e7\u00e3o e Comunica\u00e7\u00e3o, Funda\u00e7\u00e3o Oswaldo Cruz, Av.Brasil 4365, Resid\u00eancia Oficial, Manguinhos, Rio de Janeiro 21040-900, Brazil","UMR 7590, CNRS, Museum National d\u2019Histoire Naturelle, Institut de Min\u00e9ralogie, Physique des Mat\u00e9riaux et Cosmochimie, IMPMC, Sorbonne Universit\u00e9, 4 place Jussieu, Paris 75005, France"],"raw_orcid":"https://orcid.org/0000-0001-5443-286X","affiliations":[{"raw_affiliation_string":"Laboratoire de Biologie et Pharmacologie Appliqu\u00e9e, UMR 8113, \u00c9cole Normale Sup\u00e9rieure Paris-Saclay, Gif-sur-Yvette 91190, France","institution_ids":["https://openalex.org/I4210150317","https://openalex.org/I11559806"]},{"raw_affiliation_string":"Programa de Computa\u00e7\u00e3o Cient\u00edfica, Vice-Presid\u00eancia de Educa\u00e7\u00e3o, Informa\u00e7\u00e3o e Comunica\u00e7\u00e3o, Funda\u00e7\u00e3o Oswaldo Cruz, Av.Brasil 4365, Resid\u00eancia Oficial, Manguinhos, Rio de Janeiro 21040-900, Brazil","institution_ids":["https://openalex.org/I52325"]},{"raw_affiliation_string":"UMR 7590, CNRS, Museum National d\u2019Histoire Naturelle, Institut de Min\u00e9ralogie, Physique des Mat\u00e9riaux et Cosmochimie, IMPMC, Sorbonne Universit\u00e9, 4 place Jussieu, Paris 75005, France","institution_ids":["https://openalex.org/I39804081","https://openalex.org/I4210145605","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5031703110","https://openalex.org/A5043151942"],"corresponding_institution_ids":["https://openalex.org/I11559806","https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210145605","https://openalex.org/I4210150317","https://openalex.org/I52325"],"apc_list":null,"apc_paid":null,"fwci":1.2039,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.78035715,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"64","issue":"13","first_page":"5151","last_page":"5160"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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":0.9993000030517578,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9972000122070312,"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":0.9908000230789185,"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/overfitting","display_name":"Overfitting","score":0.9222478866577148},{"id":"https://openalex.org/keywords/maxima-and-minima","display_name":"Maxima and minima","score":0.7074315547943115},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6188256144523621},{"id":"https://openalex.org/keywords/mode","display_name":"Mode (computer interface)","score":0.5509117245674133},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5235388278961182},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5040408968925476},{"id":"https://openalex.org/keywords/normal-mode","display_name":"Normal mode","score":0.48888057470321655},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4495767056941986},{"id":"https://openalex.org/keywords/curve-fitting","display_name":"Curve fitting","score":0.437433660030365},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30218935012817383},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.21947714686393738},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1758469045162201},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17035958170890808},{"id":"https://openalex.org/keywords/vibration","display_name":"Vibration","score":0.1341809332370758},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.12463521957397461}],"concepts":[{"id":"https://openalex.org/C22019652","wikidata":"https://www.wikidata.org/wiki/Q331309","display_name":"Overfitting","level":3,"score":0.9222478866577148},{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.7074315547943115},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6188256144523621},{"id":"https://openalex.org/C48677424","wikidata":"https://www.wikidata.org/wiki/Q6888088","display_name":"Mode (computer interface)","level":2,"score":0.5509117245674133},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5235388278961182},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5040408968925476},{"id":"https://openalex.org/C32758168","wikidata":"https://www.wikidata.org/wiki/Q900488","display_name":"Normal mode","level":3,"score":0.48888057470321655},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4495767056941986},{"id":"https://openalex.org/C184389593","wikidata":"https://www.wikidata.org/wiki/Q603159","display_name":"Curve fitting","level":2,"score":0.437433660030365},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30218935012817383},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.21947714686393738},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1758469045162201},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17035958170890808},{"id":"https://openalex.org/C198394728","wikidata":"https://www.wikidata.org/wiki/Q3695508","display_name":"Vibration","level":2,"score":0.1341809332370758},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.12463521957397461},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"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.3c02007","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c02007","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c02007","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:38907694","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38907694","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:pubmedcentral.nih.gov:11234365","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11234365","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11234365/pdf/ci3c02007.pdf","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,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.3c02007","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c02007","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c02007","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5799999833106995,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G4894748584","display_name":null,"funder_award_id":"873/2017","funder_id":"https://openalex.org/F4320321091","funder_display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"}],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320330232","display_name":"Sorbonne Universit\u00e9","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4399916751.pdf"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W1968991415","https://openalex.org/W1972244704","https://openalex.org/W1983673980","https://openalex.org/W1989161865","https://openalex.org/W1990877090","https://openalex.org/W2021419438","https://openalex.org/W2028174524","https://openalex.org/W2029667189","https://openalex.org/W2035687084","https://openalex.org/W2038758364","https://openalex.org/W2056331547","https://openalex.org/W2059928115","https://openalex.org/W2069867742","https://openalex.org/W2072973641","https://openalex.org/W2075506230","https://openalex.org/W2093397531","https://openalex.org/W2097294533","https://openalex.org/W2100455255","https://openalex.org/W2102725267","https://openalex.org/W2103945336","https://openalex.org/W2106140689","https://openalex.org/W2113994268","https://openalex.org/W2124483575","https://openalex.org/W2130479394","https://openalex.org/W2132262459","https://openalex.org/W2132629607","https://openalex.org/W2141205833","https://openalex.org/W2150008490","https://openalex.org/W2150981663","https://openalex.org/W2154319440","https://openalex.org/W2159211495","https://openalex.org/W2161252555","https://openalex.org/W2180229411","https://openalex.org/W2180441778","https://openalex.org/W2250722998","https://openalex.org/W2265101181","https://openalex.org/W2315101055","https://openalex.org/W2322463084","https://openalex.org/W2469449201","https://openalex.org/W2491917380","https://openalex.org/W2555870966","https://openalex.org/W2563915892","https://openalex.org/W2582743722","https://openalex.org/W2604948333","https://openalex.org/W2759539894","https://openalex.org/W2765322245","https://openalex.org/W2805621788","https://openalex.org/W2886486369","https://openalex.org/W2905879613","https://openalex.org/W2918297620","https://openalex.org/W2999450023","https://openalex.org/W3114912800","https://openalex.org/W3200545562","https://openalex.org/W4210877737","https://openalex.org/W4214537095","https://openalex.org/W4214673765","https://openalex.org/W4214733723","https://openalex.org/W4221015365","https://openalex.org/W4225836667","https://openalex.org/W4283790249","https://openalex.org/W4313887203","https://openalex.org/W4318943895","https://openalex.org/W4366609148","https://openalex.org/W4386407015","https://openalex.org/W4386913014","https://openalex.org/W4387230705"],"related_works":["https://openalex.org/W4362597605","https://openalex.org/W1574414179","https://openalex.org/W4297676672","https://openalex.org/W3009056573","https://openalex.org/W2922073769","https://openalex.org/W4281702477","https://openalex.org/W2490526372","https://openalex.org/W4376166922","https://openalex.org/W4378510483","https://openalex.org/W4221142204"],"abstract_inverted_index":{"Molecular":[0],"Dynamics":[1],"Flexible":[2],"Fitting":[3],"(MDFF)":[4],"is":[5,23,121],"a":[6,63],"widely":[7],"used":[8],"tool":[9],"to":[10,37,95],"refine":[11],"high-resolution":[12],"structures":[13],"into":[14],"cryo-EM":[15],"density":[16],"maps.":[17],"Despite":[18],"many":[19],"successful":[20],"applications,":[21],"MDFF":[22,45],"still":[24],"limited":[25],"by":[26],"its":[27],"high":[28],"computational":[29],"cost,":[30],"overfitting,":[31],"accuracy,":[32],"and":[33,74,117],"performance":[34],"issues":[35],"due":[36],"entrapment":[38],"within":[39],"wrong":[40],"local":[41],"minima.":[42],"Modern":[43],"ensemble-based":[44],"tools":[46],"have":[47],"generated":[48],"promising":[49],"results":[50],"in":[51,102],"the":[52,84,89,96],"past":[53],"decade.":[54],"In":[55],"line":[56],"with":[57,105,113],"these":[58],"studies,":[59],"we":[60],"present":[61],"MDFF_NM,":[62],"stochastic":[64],"hybrid":[65],"flexible":[66,76],"fitting":[67,85,92],"algorithm":[68],"combining":[69],"Normal":[70],"Mode":[71],"Analysis":[72],"(NMA)":[73],"simulation-based":[75],"fitting.":[77],"Initial":[78],"tests":[79],"reveal":[80],"that,":[81],"besides":[82],"accelerating":[83],"process,":[86],"MDFF_NM":[87,112],"increases":[88],"diversity":[90],"of":[91,100,111],"routes":[93],"leading":[94],"target,":[97],"uncovering":[98],"ensembles":[99],"conformations":[101],"closer":[103],"agreement":[104],"experimental":[106],"data.":[107],"The":[108],"potential":[109],"integration":[110],"other":[114],"existing":[115],"methods":[116],"integrative":[118],"modeling":[119],"pipelines":[120],"also":[122],"discussed.":[123]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4}],"updated_date":"2026-06-21T07:57:09.225873","created_date":"2025-10-10T00:00:00"}