{"id":"https://openalex.org/W4416395846","doi":"https://doi.org/10.1021/acs.jcim.5c02413","title":"eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems","display_name":"eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems","publication_year":2025,"publication_date":"2025-11-19","ids":{"openalex":"https://openalex.org/W4416395846","doi":"https://doi.org/10.1021/acs.jcim.5c02413","pmid":"https://pubmed.ncbi.nlm.nih.gov/41254899"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02413","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02413","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c02413?ref=article_openPDF","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":"software-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c02413?ref=article_openPDF","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051123981","display_name":"Pablo R. Arantes","orcid":"https://orcid.org/0000-0003-1946-2750"},"institutions":[{"id":"https://openalex.org/I134363262","display_name":"Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre","ror":"https://ror.org/00x0nkm13","country_code":"BR","type":"education","lineage":["https://openalex.org/I134363262"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Pablo Ricardo Arantes","raw_affiliation_strings":["Graduate Program in Biosciences (PPG Bio), Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre (UFCSPA); Rua Sarmento Leite, 245 - Centro Hist\u00f3rico, Porto Alegre 90050-170, Brasil"],"raw_orcid":"https://orcid.org/0000-0003-1946-2750","affiliations":[{"raw_affiliation_string":"Graduate Program in Biosciences (PPG Bio), Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre (UFCSPA); Rua Sarmento Leite, 245 - Centro Hist\u00f3rico, Porto Alegre 90050-170, Brasil","institution_ids":["https://openalex.org/I134363262"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066200129","display_name":"Rodrigo Ligabue\u2010Braun","orcid":"https://orcid.org/0000-0002-2555-9754"},"institutions":[{"id":"https://openalex.org/I134363262","display_name":"Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre","ror":"https://ror.org/00x0nkm13","country_code":"BR","type":"education","lineage":["https://openalex.org/I134363262"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Rodrigo Ligabue-Braun","raw_affiliation_strings":["Graduate Program in Biosciences (PPG Bio), Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre (UFCSPA); Rua Sarmento Leite, 245 - Centro Hist\u00f3rico, Porto Alegre 90050-170, Brasil"],"raw_orcid":"https://orcid.org/0000-0002-2555-9754","affiliations":[{"raw_affiliation_string":"Graduate Program in Biosciences (PPG Bio), Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre (UFCSPA); Rua Sarmento Leite, 245 - Centro Hist\u00f3rico, Porto Alegre 90050-170, Brasil","institution_ids":["https://openalex.org/I134363262"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067913606","display_name":"Conrado Pedebos","orcid":"https://orcid.org/0000-0003-0378-4851"},"institutions":[{"id":"https://openalex.org/I134363262","display_name":"Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre","ror":"https://ror.org/00x0nkm13","country_code":"BR","type":"education","lineage":["https://openalex.org/I134363262"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Conrado Pedebos","raw_affiliation_strings":["Graduate Program in Biosciences (PPG Bio), Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre (UFCSPA); Rua Sarmento Leite, 245 - Centro Hist\u00f3rico, Porto Alegre 90050-170, Brasil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate Program in Biosciences (PPG Bio), Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre (UFCSPA); Rua Sarmento Leite, 245 - Centro Hist\u00f3rico, Porto Alegre 90050-170, Brasil","institution_ids":["https://openalex.org/I134363262"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5051123981"],"corresponding_institution_ids":["https://openalex.org/I134363262"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"65","issue":"23","first_page":"12648","last_page":"12654"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8842999935150146,"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":0.8842999935150146,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.02879999950528145,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.011099999770522118,"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/python","display_name":"Python (programming language)","score":0.8765000104904175},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6657999753952026},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.6245999932289124},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5033000111579895},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"Conformational ensembles","score":0.4578000009059906},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"Ensemble learning","score":0.40139999985694885}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8765000104904175},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7246000170707703},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6657999753952026},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.6245999932289124},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5033000111579895},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.4578000009059906},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4359000027179718},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.40139999985694885},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35019999742507935},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3472999930381775},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3330000042915344},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.31869998574256897},{"id":"https://openalex.org/C38111792","wikidata":"https://www.wikidata.org/wiki/Q15712714","display_name":"Biomolecular structure","level":3,"score":0.302700012922287},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.29499998688697815},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.27390000224113464},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27309998869895935},{"id":"https://openalex.org/C11577676","wikidata":"https://www.wikidata.org/wiki/Q134237","display_name":"Square root","level":2,"score":0.2612000107765198},{"id":"https://openalex.org/C32833848","wikidata":"https://www.wikidata.org/wiki/Q4115054","display_name":"Extensibility","level":2,"score":0.25360000133514404}],"mesh":[{"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":3,"locations":[{"id":"doi:10.1021/acs.jcim.5c02413","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02413","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c02413?ref=article_openPDF","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:41254899","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41254899","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:12690589","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12690589/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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.5c02413","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02413","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c02413?ref=article_openPDF","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":[],"awards":[{"id":"https://openalex.org/G6994101484","display_name":null,"funder_award_id":"150566/2024-7","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"}],"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/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320322502","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado do Rio Grande do Sul","ror":"https://ror.org/05k49za97"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4416395846.pdf","grobid_xml":"https://content.openalex.org/works/W4416395846.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1931545954","https://openalex.org/W1989161865","https://openalex.org/W2039630680","https://openalex.org/W2085915283","https://openalex.org/W2112959255","https://openalex.org/W2154319440","https://openalex.org/W2170711116","https://openalex.org/W2510475640","https://openalex.org/W2515002494","https://openalex.org/W2940819419","https://openalex.org/W2967689183","https://openalex.org/W3094098207","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3203800312","https://openalex.org/W4221090934","https://openalex.org/W4229658977","https://openalex.org/W4281790889","https://openalex.org/W4385627674","https://openalex.org/W4393092828","https://openalex.org/W4393233076","https://openalex.org/W4403340940","https://openalex.org/W4412165572"],"related_works":[],"abstract_inverted_index":{"Understanding":[0],"molecular":[1,49],"flexibility":[2,54],"and":[3,25,80,107,137],"dynamics":[4,50],"across":[5,90],"different":[6,60],"structural":[7],"ensembles":[8,57],"is":[9,150],"essential":[10],"for":[11,71,148],"interpreting":[12],"the":[13],"behavior":[14],"of":[15],"complex":[16],"biological":[17],"systems.":[18],"Here,":[19],"we":[20],"introduce":[21],"eRMSF,":[22],"a":[23,95],"fast":[24],"user-friendly":[26],"Python":[27],"package":[28],"built":[29],"with":[30],"MDAKit":[31],"from":[32],"MDAnalysis,":[33],"designed":[34],"to":[35,48,56,98,121],"perform":[36],"ensemble-based":[37],"root":[38],"mean":[39],"square":[40],"fluctuation":[41],"(RMSF)":[42],"analyses.":[43,145],"Unlike":[44],"traditional":[45],"approaches":[46],"limited":[47],"trajectories,":[51],"eRMSF":[52,93,149],"extends":[53],"analysis":[55],"generated":[58],"by":[59,143],"methods,":[61],"such":[62],"as":[63],"MD":[64],"simulations,":[65],"BioEmu":[66],"(a":[67],"deep":[68],"learning":[69],"tool":[70],"equilibrium":[72],"ensemble":[73,78],"prediction),":[74],"subsampled":[75],"AlphaFold2":[76],"(AlphaFold":[77],"generation),":[79],"other":[81],"computational":[82],"or":[83,101,116],"experimental":[84],"sources.":[85],"By":[86],"enabling":[87],"RMSF":[88],"calculations":[89],"heterogeneous":[91],"ensembles,":[92],"provides":[94],"unified":[96],"framework":[97],"evaluate":[99],"residue":[100],"atomic":[102],"fluctuations":[103],"in":[104],"both":[105],"simulated":[106],"predicted":[108],"structures.":[109],"Users":[110],"can":[111],"easily":[112],"customize":[113],"atom,":[114],"residue,":[115],"region":[117],"selections,":[118],"tailoring":[119],"analyses":[120],"specific":[122],"research":[123],"questions.":[124],"This":[125],"approach":[126],"delivers":[127],"high-resolution":[128],"insights":[129],"into":[130],"localized":[131],"motions,":[132],"complements":[133],"global":[134],"stability":[135],"assessments,":[136],"reveals":[138],"dynamic":[139],"regions":[140],"often":[141],"overlooked":[142],"single-method":[144],"The":[146],"repository":[147],"available":[151],"at":[152],"https://github.com/pablo-arantes/ermsfkit.":[153]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-11-19T00:00:00"}
