{"id":"https://openalex.org/W4383483775","doi":"https://doi.org/10.1093/bib/bbad242","title":"EnGens: a computational framework for generation and analysis of representative protein conformational ensembles","display_name":"EnGens: a computational framework for generation and analysis of representative protein conformational ensembles","publication_year":2023,"publication_date":"2023-06-18","ids":{"openalex":"https://openalex.org/W4383483775","doi":"https://doi.org/10.1093/bib/bbad242","pmid":"https://pubmed.ncbi.nlm.nih.gov/37418278"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad242","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad242","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad242/50827797/bbad242.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad242/50827797/bbad242.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066354975","display_name":"Anja Conev","orcid":"https://orcid.org/0000-0001-9049-0266"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anja Conev","raw_affiliation_strings":["Rice University Department of Computer Science, , Houston 77005, TX, USA"],"raw_orcid":"https://orcid.org/0000-0001-9049-0266","affiliations":[{"raw_affiliation_string":"Rice University Department of Computer Science, , Houston 77005, TX, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034774826","display_name":"Maur\u00edcio Rigo","orcid":"https://orcid.org/0000-0002-1584-6194"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mauricio Menegatti Rigo","raw_affiliation_strings":["Rice University Department of Computer Science, , Houston 77005, TX , USA"],"raw_orcid":"https://orcid.org/0000-0002-1584-6194","affiliations":[{"raw_affiliation_string":"Rice University Department of Computer Science, , Houston 77005, TX , USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090227170","display_name":"Didier Devaurs","orcid":"https://orcid.org/0000-0002-3415-9816"},"institutions":[{"id":"https://openalex.org/I4210158898","display_name":"Institute of Genetics and Cancer","ror":"https://ror.org/05hygey35","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210087105","https://openalex.org/I4210158898","https://openalex.org/I90344618","https://openalex.org/I98677209"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Didier Devaurs","raw_affiliation_strings":["University of Edinburgh MRC Institute of Genetics and Cancer, , Edinburgh EH4 2XU , UK"],"raw_orcid":"https://orcid.org/0000-0002-3415-9816","affiliations":[{"raw_affiliation_string":"University of Edinburgh MRC Institute of Genetics and Cancer, , Edinburgh EH4 2XU , UK","institution_ids":["https://openalex.org/I4210158898","https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112376984","display_name":"Andr\u00e9 Faustino Fonseca","orcid":null},"institutions":[{"id":"https://openalex.org/I44461941","display_name":"University of Houston","ror":"https://ror.org/048sx0r50","country_code":"US","type":"education","lineage":["https://openalex.org/I44461941"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andr\u00e9 Faustino Fonseca","raw_affiliation_strings":["University of Houston Department of Biology and Biochemistry, , Houston 77004, TX , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Houston Department of Biology and Biochemistry, , Houston 77004, TX , USA","institution_ids":["https://openalex.org/I44461941"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000923052","display_name":"Hussain Kalavadwala","orcid":null},"institutions":[{"id":"https://openalex.org/I44461941","display_name":"University of Houston","ror":"https://ror.org/048sx0r50","country_code":"US","type":"education","lineage":["https://openalex.org/I44461941"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hussain Kalavadwala","raw_affiliation_strings":["University of Houston Department of Biology and Biochemistry, , Houston 77004, TX , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Houston Department of Biology and Biochemistry, , Houston 77004, TX , USA","institution_ids":["https://openalex.org/I44461941"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065138381","display_name":"Martiela Vaz de Freitas","orcid":"https://orcid.org/0000-0003-4178-6604"},"institutions":[{"id":"https://openalex.org/I44461941","display_name":"University of Houston","ror":"https://ror.org/048sx0r50","country_code":"US","type":"education","lineage":["https://openalex.org/I44461941"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martiela Vaz de Freitas","raw_affiliation_strings":["University of Houston Department of Biology and Biochemistry, , Houston 77004, TX , USA"],"raw_orcid":"https://orcid.org/0000-0003-4178-6604","affiliations":[{"raw_affiliation_string":"University of Houston Department of Biology and Biochemistry, , Houston 77004, TX , USA","institution_ids":["https://openalex.org/I44461941"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061903235","display_name":"Cecilia Clementi","orcid":"https://orcid.org/0000-0001-9221-2358"},"institutions":[{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Cecilia Clementi","raw_affiliation_strings":["Freie Universit\u00e4t Berlin Department of Physics, , Berlin 14195 , Germany"],"raw_orcid":"https://orcid.org/0000-0001-9221-2358","affiliations":[{"raw_affiliation_string":"Freie Universit\u00e4t Berlin Department of Physics, , Berlin 14195 , Germany","institution_ids":["https://openalex.org/I75951250"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036942740","display_name":"Geancarlo Zanatta","orcid":"https://orcid.org/0000-0003-0111-5347"},"institutions":[{"id":"https://openalex.org/I130442723","display_name":"Universidade Federal do Rio Grande do Sul","ror":"https://ror.org/041yk2d64","country_code":"BR","type":"education","lineage":["https://openalex.org/I130442723"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Geancarlo Zanatta","raw_affiliation_strings":["Institute of Biosciences, Federal University of Rio Grande do Sul Department of Biophysics, , Porto Alegre 91501-970 , Brazil"],"raw_orcid":"https://orcid.org/0000-0003-0111-5347","affiliations":[{"raw_affiliation_string":"Institute of Biosciences, Federal University of Rio Grande do Sul Department of Biophysics, , Porto Alegre 91501-970 , Brazil","institution_ids":["https://openalex.org/I130442723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015688397","display_name":"Dinler A. Antunes","orcid":"https://orcid.org/0000-0001-7947-6455"},"institutions":[{"id":"https://openalex.org/I44461941","display_name":"University of Houston","ror":"https://ror.org/048sx0r50","country_code":"US","type":"education","lineage":["https://openalex.org/I44461941"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dinler Amaral Antunes","raw_affiliation_strings":["University of Houston Department of Biology and Biochemistry, , Houston 77004, TX , USA"],"raw_orcid":"https://orcid.org/0000-0001-7947-6455","affiliations":[{"raw_affiliation_string":"University of Houston Department of Biology and Biochemistry, , Houston 77004, TX , USA","institution_ids":["https://openalex.org/I44461941"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067205988","display_name":"Lydia E. Kavraki","orcid":"https://orcid.org/0000-0003-0699-8038"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lydia E Kavraki","raw_affiliation_strings":["Rice University Department of Computer Science, , Houston 77005, TX , USA"],"raw_orcid":"https://orcid.org/0000-0003-0699-8038","affiliations":[{"raw_affiliation_string":"Rice University Department of Computer Science, , Houston 77005, TX , USA","institution_ids":["https://openalex.org/I74775410"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5015688397","https://openalex.org/A5067205988"],"corresponding_institution_ids":["https://openalex.org/I44461941","https://openalex.org/I74775410"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.2002,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.88603215,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"24","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"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":0.9990000128746033,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9817000031471252,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9815000295639038,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5560570359230042},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3688853681087494},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3413616418838501},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12065508961677551}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5560570359230042},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3688853681087494},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3413616418838501},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12065508961677551}],"mesh":[{"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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},{"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":6,"locations":[{"id":"doi:10.1093/bib/bbad242","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad242","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad242/50827797/bbad242.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37418278","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37418278","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":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10359083","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10359083","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10359083/pdf/bbad242.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:pure.ed.ac.uk:openaire/2cf2fdb6-2f8e-4eef-b0f5-ac14673911bd","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/2cf2fdb6-2f8e-4eef-b0f5-ac14673911bd","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Conev, A, Rigo, M M, Devaurs, D, Fonseca, A F, Kalavadwala, H, de Freitas, M V, Clementi, C, Zanatta, G, Antunes, D A & Kavraki, L E 2023, 'EnGens : a computational framework for generation and analysis of representative protein conformational ensembles', Briefings in bioinformatics, vol. 24, no. 4, bbad242. https://doi.org/10.1093/bib/bbad242","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pure.ed.ac.uk:publications/2cf2fdb6-2f8e-4eef-b0f5-ac14673911bd","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/files/458738788/bbad242.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Conev, A, Rigo, M M, Devaurs, D, Fonseca, A F, Kalavadwala, H, de Freitas, M V, Clementi, C, Zanatta, G, Antunes, D A & Kavraki, L E 2023, 'EnGens : a computational framework for generation and analysis of representative protein conformational ensembles', Briefings in bioinformatics, vol. 24, no. 4, bbad242. https://doi.org/10.1093/bib/bbad242","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:repository.rice.edu:1911/115042","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad242.","pdf_url":null,"source":{"id":"https://openalex.org/S4306401268","display_name":"Rice Digital Scholarship Archive (Rice University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I74775410","host_organization_name":"Rice University","host_organization_lineage":["https://openalex.org/I74775410"],"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":"Journal article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad242","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad242","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad242/50827797/bbad242.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1329410657","display_name":null,"funder_award_id":"#440412/2022-6","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G1960506700","display_name":"PROTEAN-CR: Proteomics Toolkit for Ensemble Analysis in Cancer Research","funder_award_id":"5u01ca258512-03","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G500871726","display_name":null,"funder_award_id":"RP170593","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7583090230","display_name":null,"funder_award_id":"MC_UU_00009/2","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G7631811596","display_name":"Cross-disciplinary post-doctoral fellow training scheme in quantative biomedicine (XDF) - 8 x 4 year post-docs","funder_award_id":"MC_UU_00009/2","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G8946597769","display_name":null,"funder_award_id":"U01 CA258512","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320310133","display_name":"Rice University","ror":"https://ror.org/008zs3103"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4383483775.pdf","grobid_xml":"https://content.openalex.org/works/W4383483775.grobid-xml"},"referenced_works_count":83,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1875037981","https://openalex.org/W1973996451","https://openalex.org/W1976203248","https://openalex.org/W1977556410","https://openalex.org/W1981021420","https://openalex.org/W2001764614","https://openalex.org/W2004303971","https://openalex.org/W2027361781","https://openalex.org/W2041205020","https://openalex.org/W2046898277","https://openalex.org/W2048537273","https://openalex.org/W2048822589","https://openalex.org/W2052262181","https://openalex.org/W2054318449","https://openalex.org/W2066270419","https://openalex.org/W2076223436","https://openalex.org/W2084509457","https://openalex.org/W2085213650","https://openalex.org/W2094795801","https://openalex.org/W2101234009","https://openalex.org/W2103325328","https://openalex.org/W2114850508","https://openalex.org/W2119394534","https://openalex.org/W2123681603","https://openalex.org/W2132262459","https://openalex.org/W2137076421","https://openalex.org/W2143592395","https://openalex.org/W2147466870","https://openalex.org/W2147988069","https://openalex.org/W2158476854","https://openalex.org/W2158703410","https://openalex.org/W2220469999","https://openalex.org/W2226825552","https://openalex.org/W2294798173","https://openalex.org/W2552763360","https://openalex.org/W2620849404","https://openalex.org/W2775004427","https://openalex.org/W2783073729","https://openalex.org/W2804043881","https://openalex.org/W2892940574","https://openalex.org/W2898210859","https://openalex.org/W2949223833","https://openalex.org/W2954046734","https://openalex.org/W2964917500","https://openalex.org/W2969604201","https://openalex.org/W2977466517","https://openalex.org/W3008926066","https://openalex.org/W3045213745","https://openalex.org/W3046751266","https://openalex.org/W3048799182","https://openalex.org/W3084247016","https://openalex.org/W3087024315","https://openalex.org/W3100211935","https://openalex.org/W3100810942","https://openalex.org/W3102499948","https://openalex.org/W3104537585","https://openalex.org/W3105774298","https://openalex.org/W3140562424","https://openalex.org/W3159156584","https://openalex.org/W3162048346","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3203596047","https://openalex.org/W3207537951","https://openalex.org/W3211795435","https://openalex.org/W3215883361","https://openalex.org/W4221147630","https://openalex.org/W4226094936","https://openalex.org/W4229455959","https://openalex.org/W4281942705","https://openalex.org/W4283757661","https://openalex.org/W4285741880","https://openalex.org/W4297896120","https://openalex.org/W4306670540","https://openalex.org/W4310882530","https://openalex.org/W4323537970","https://openalex.org/W4327550249","https://openalex.org/W4389920712","https://openalex.org/W6644682428","https://openalex.org/W6675354045","https://openalex.org/W6802922870","https://openalex.org/W6840065848"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Proteins":[0],"are":[1],"dynamic":[2],"macromolecules":[3],"that":[4],"perform":[5],"vital":[6],"functions":[7],"in":[8,76,84,164],"cells.":[9],"A":[10],"protein":[11,60,136,154,215],"structure":[12,18],"determines":[13],"its":[14],"function,":[15],"but":[16],"this":[17,140],"is":[19,37,102],"not":[20,103],"static,":[21],"as":[22,70,207],"proteins":[23,36],"change":[24],"their":[25,41],"conformation":[26],"to":[27,39,67,81,113],"achieve":[28],"various":[29],"functions.":[30],"Understanding":[31],"the":[32,85,192,220],"conformational":[33,72,92,97,137],"landscapes":[34,54],"of":[35,43,46,87,147,214,219,222],"essential":[38],"understand":[40],"mechanism":[42],"action.":[44],"Sets":[45],"carefully":[47],"chosen":[48],"conformations":[49],"can":[50,199],"summarize":[51],"such":[52,100,206],"complex":[53],"and":[55,107,133,150,158,169,217],"provide":[56,144],"better":[57],"insights":[58],"into":[59,127],"function":[61],"than":[62],"single":[63],"conformations.":[64],"We":[65],"refer":[66],"these":[68,125],"sets":[69],"representative":[71,96,135,153],"ensembles.":[73,138],"Recent":[74],"advances":[75],"computational":[77],"methods":[78,109,126,149],"have":[79,110],"led":[80],"an":[82,104,145,165],"increase":[83],"number":[86],"available":[88],"structural":[89,155],"datasets":[90,101],"spanning":[91],"landscapes.":[93],"However,":[94],"extracting":[95],"ensembles":[98,195],"from":[99,191],"easy":[105],"task":[106],"many":[108,203],"been":[111],"developed":[112],"tackle":[114],"it.":[115],"Our":[116],"new":[117],"approach,":[118],"EnGens":[119,198],"(short":[120],"for":[121,131,152,202],"ensemble":[122,156,209],"generation),":[123],"collects":[124],"a":[128,170,178,187],"unified":[129],"framework":[130],"generating":[132],"analyzing":[134],"In":[139],"work,":[141],"we:":[142],"(1)":[143],"overview":[146],"existing":[148,162],"tools":[151],"generation":[157],"analysis;":[159],"(2)":[160],"unify":[161],"approaches":[163],"open-source":[166],"Python":[167],"package,":[168],"portable":[171],"Docker":[172],"image,":[173],"providing":[174],"interactive":[175],"visualizations":[176],"within":[177],"Jupyter":[179],"Notebook":[180],"pipeline;":[181],"(3)":[182],"test":[183],"our":[184],"pipeline":[185],"on":[186],"few":[188],"canonical":[189],"examples":[190],"literature.":[193],"Representative":[194],"produced":[196],"by":[197],"be":[200],"used":[201],"downstream":[204],"tasks":[205],"protein-ligand":[208],"docking,":[210],"Markov":[211],"state":[212],"modeling":[213],"dynamics":[216],"analysis":[218],"effect":[221],"single-point":[223],"mutations.":[224]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
