{"id":"https://openalex.org/W4412548983","doi":"https://doi.org/10.1021/acs.jcim.5c01226","title":"SIRAH Tools GUI: An Intuitive Interface for the Analysis of CG Simulations","display_name":"SIRAH Tools GUI: An Intuitive Interface for the Analysis of CG Simulations","publication_year":2025,"publication_date":"2025-07-22","ids":{"openalex":"https://openalex.org/W4412548983","doi":"https://doi.org/10.1021/acs.jcim.5c01226","pmid":"https://pubmed.ncbi.nlm.nih.gov/40692309"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c01226","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01226","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/A5060513065","display_name":"Andr\u00e9s Ballesteros\u2010Casallas","orcid":"https://orcid.org/0000-0003-2421-7952"},"institutions":[{"id":"https://openalex.org/I180910786","display_name":"Universidad de la Rep\u00fablica de Uruguay","ror":"https://ror.org/030bbe882","country_code":"UY","type":"education","lineage":["https://openalex.org/I180910786"]},{"id":"https://openalex.org/I4210156231","display_name":"Institut Pasteur de Montevideo","ror":"https://ror.org/04dpm2z73","country_code":"UY","type":"facility","lineage":["https://openalex.org/I4210156231"]},{"id":"https://openalex.org/I4210166370","display_name":"Universidad La Rep\u00fablica","ror":"https://ror.org/05xs36f43","country_code":"CL","type":"education","lineage":["https://openalex.org/I4210166370"]}],"countries":["CL","UY"],"is_corresponding":false,"raw_author_name":"Andr\u00e9s Ballesteros-Casallas","raw_affiliation_strings":["Institut Pasteur de Montevideo","Universidad de la Rep\u00fablica","\u00c1rea Bioinform\u00e1tica, Departamento DETEMA, Facultad de Qu\u00edmica"],"affiliations":[{"raw_affiliation_string":"Institut Pasteur de Montevideo","institution_ids":["https://openalex.org/I4210156231"]},{"raw_affiliation_string":"Universidad de la Rep\u00fablica","institution_ids":["https://openalex.org/I4210166370","https://openalex.org/I180910786"]},{"raw_affiliation_string":"\u00c1rea Bioinform\u00e1tica, Departamento DETEMA, Facultad de Qu\u00edmica","institution_ids":["https://openalex.org/I180910786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103917165","display_name":"Antonella Alba","orcid":null},"institutions":[{"id":"https://openalex.org/I4210156231","display_name":"Institut Pasteur de Montevideo","ror":"https://ror.org/04dpm2z73","country_code":"UY","type":"facility","lineage":["https://openalex.org/I4210156231"]}],"countries":["UY"],"is_corresponding":false,"raw_author_name":"Antonella Alba","raw_affiliation_strings":["Institut Pasteur de Montevideo"],"affiliations":[{"raw_affiliation_string":"Institut Pasteur de Montevideo","institution_ids":["https://openalex.org/I4210156231"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055201436","display_name":"Jorge Cantero","orcid":"https://orcid.org/0000-0002-2304-1396"},"institutions":[{"id":"https://openalex.org/I180910786","display_name":"Universidad de la Rep\u00fablica de Uruguay","ror":"https://ror.org/030bbe882","country_code":"UY","type":"education","lineage":["https://openalex.org/I180910786"]},{"id":"https://openalex.org/I4210098779","display_name":"Universidad Nacional del Este","ror":"https://ror.org/00xwv4z20","country_code":"PY","type":"education","lineage":["https://openalex.org/I4210098779"]},{"id":"https://openalex.org/I4210098917","display_name":"Instituto de Investigaciones en Ciencias de la Salud","ror":"https://ror.org/00vsnbn30","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I166401450","https://openalex.org/I4210098917","https://openalex.org/I4210123736","https://openalex.org/I4210130626","https://openalex.org/I4387155568"]},{"id":"https://openalex.org/I4210152408","display_name":"Centro de Investigaciones Cardiovasculares","ror":"https://ror.org/04ebzxq58","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4210138160","https://openalex.org/I4210152408","https://openalex.org/I4387155568","https://openalex.org/I874386039"]},{"id":"https://openalex.org/I4210153181","display_name":"Universidad de Ciencias M\u00e9dicas de la Habana","ror":"https://ror.org/04kgp9g48","country_code":"CU","type":"education","lineage":["https://openalex.org/I4210122314","https://openalex.org/I4210153181"]},{"id":"https://openalex.org/I4210166370","display_name":"Universidad La Rep\u00fablica","ror":"https://ror.org/05xs36f43","country_code":"CL","type":"education","lineage":["https://openalex.org/I4210166370"]}],"countries":["AR","CL","CU","PY","UY"],"is_corresponding":false,"raw_author_name":"Jorge Cantero","raw_affiliation_strings":["Centro de Investigaciones M\u00e9dicas, Facultad de Ciencias de la Salud","Universidad Nacional del Este","Universidad de la Rep\u00fablica","\u00c1rea Bioinform\u00e1tica, Departamento DETEMA, Facultad de Qu\u00edmica"],"affiliations":[{"raw_affiliation_string":"Centro de Investigaciones M\u00e9dicas, Facultad de Ciencias de la Salud","institution_ids":["https://openalex.org/I4210153181","https://openalex.org/I4210098917","https://openalex.org/I4210152408"]},{"raw_affiliation_string":"Universidad Nacional del Este","institution_ids":["https://openalex.org/I4210098779"]},{"raw_affiliation_string":"Universidad de la Rep\u00fablica","institution_ids":["https://openalex.org/I4210166370","https://openalex.org/I180910786"]},{"raw_affiliation_string":"\u00c1rea Bioinform\u00e1tica, Departamento DETEMA, Facultad de Qu\u00edmica","institution_ids":["https://openalex.org/I180910786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069266246","display_name":"Mart\u00edn S\u00f3\u00f1ora","orcid":"https://orcid.org/0000-0003-3872-6117"},"institutions":[{"id":"https://openalex.org/I4210156231","display_name":"Institut Pasteur de Montevideo","ror":"https://ror.org/04dpm2z73","country_code":"UY","type":"facility","lineage":["https://openalex.org/I4210156231"]}],"countries":["UY"],"is_corresponding":false,"raw_author_name":"Mart\u00edn So\u00f1ora","raw_affiliation_strings":["Institut Pasteur de Montevideo"],"affiliations":[{"raw_affiliation_string":"Institut Pasteur de Montevideo","institution_ids":["https://openalex.org/I4210156231"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018426427","display_name":"Lucianna Helene Santos","orcid":"https://orcid.org/0000-0002-6910-0697"},"institutions":[{"id":"https://openalex.org/I4210156231","display_name":"Institut Pasteur de Montevideo","ror":"https://ror.org/04dpm2z73","country_code":"UY","type":"facility","lineage":["https://openalex.org/I4210156231"]}],"countries":["UY"],"is_corresponding":true,"raw_author_name":"Lucianna H. S. Santos","raw_affiliation_strings":["Institut Pasteur de Montevideo"],"affiliations":[{"raw_affiliation_string":"Institut Pasteur de Montevideo","institution_ids":["https://openalex.org/I4210156231"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035123082","display_name":"Sergio Pantano","orcid":"https://orcid.org/0000-0001-6435-4543"},"institutions":[{"id":"https://openalex.org/I180910786","display_name":"Universidad de la Rep\u00fablica de Uruguay","ror":"https://ror.org/030bbe882","country_code":"UY","type":"education","lineage":["https://openalex.org/I180910786"]},{"id":"https://openalex.org/I4210156231","display_name":"Institut Pasteur de Montevideo","ror":"https://ror.org/04dpm2z73","country_code":"UY","type":"facility","lineage":["https://openalex.org/I4210156231"]},{"id":"https://openalex.org/I4210166370","display_name":"Universidad La Rep\u00fablica","ror":"https://ror.org/05xs36f43","country_code":"CL","type":"education","lineage":["https://openalex.org/I4210166370"]}],"countries":["CL","UY"],"is_corresponding":false,"raw_author_name":"Sergio Pantano","raw_affiliation_strings":["Institut Pasteur de Montevideo","Universidad de la Rep\u00fablica","\u00c1rea Bioinform\u00e1tica, Departamento DETEMA, Facultad de Qu\u00edmica"],"affiliations":[{"raw_affiliation_string":"Institut Pasteur de Montevideo","institution_ids":["https://openalex.org/I4210156231"]},{"raw_affiliation_string":"Universidad de la Rep\u00fablica","institution_ids":["https://openalex.org/I4210166370","https://openalex.org/I180910786"]},{"raw_affiliation_string":"\u00c1rea Bioinform\u00e1tica, Departamento DETEMA, Facultad de Qu\u00edmica","institution_ids":["https://openalex.org/I180910786"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5018426427"],"corresponding_institution_ids":["https://openalex.org/I4210156231"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.17648274,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"65","issue":"20","first_page":"10797","last_page":"10802"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9830999970436096,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9830999970436096,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/T11450","display_name":"Model-Driven Software Engineering Techniques","score":0.9761000275611877,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9722999930381775,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/computer-science","display_name":"Computer science","score":0.6578490734100342},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5514923334121704},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5142278671264648},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.46971315145492554},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.33618271350860596},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.23617973923683167}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6578490734100342},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5514923334121704},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5142278671264648},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.46971315145492554},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.33618271350860596},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.23617973923683167},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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.5c01226","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01226","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:40692309","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40692309","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":[],"funders":[{"id":"https://openalex.org/F4320310753","display_name":"Agencia Nacional de Investigaci\u00f3n e Innovaci\u00f3n","ror":"https://ror.org/03egaj678"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W2029667189","https://openalex.org/W2079300981","https://openalex.org/W2118233996","https://openalex.org/W2147988069","https://openalex.org/W2151553287","https://openalex.org/W2292169708","https://openalex.org/W2332712348","https://openalex.org/W2510475640","https://openalex.org/W2758901838","https://openalex.org/W3010761615","https://openalex.org/W3046751266","https://openalex.org/W3206486942","https://openalex.org/W4380873918","https://openalex.org/W4387300174","https://openalex.org/W4387440676","https://openalex.org/W4392293365","https://openalex.org/W4402837486","https://openalex.org/W4411556630"],"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/W2022968056","https://openalex.org/W2993198389","https://openalex.org/W2102284328","https://openalex.org/W1555107492"],"abstract_inverted_index":{"The":[0,159],"increasing":[1],"complexity":[2],"and":[3,28,67,132],"scale":[4],"of":[5,22,30,71,114,126],"molecular":[6,13,79],"systems":[7],"pose":[8],"significant":[9],"challenges":[10],"for":[11,36,47,77,162],"all-atom":[12],"dynamics":[14],"(MD)":[15],"simulations,":[16],"leading":[17],"to":[18,40,101,155],"the":[19,69,83,112,151,156],"growing":[20],"adoption":[21],"coarse-grained":[23],"(CG)":[24],"models.":[25],"However,":[26],"visualization":[27],"analysis":[29,148],"CG":[31,105,146],"simulations":[32,80,125],"remain":[33],"challenging,":[34],"particularly":[35],"new":[37],"users,":[38],"due":[39],"limitations":[41],"in":[42],"existing":[43],"tools":[44],"designed":[45],"primarily":[46],"atomic-level":[48],"representations.":[49],"To":[50],"address":[51],"these":[52],"challenges,":[53],"we":[54,110],"present":[55],"SIRAH":[56,75,84,87,115,123,141,163],"Tools":[57,88,116,142,164],"GUI,":[58],"a":[59,127,133,138],"graphical":[60],"user":[61],"interface":[62,93],"that":[63,97],"integrates":[64],"with":[65,82,94],"VMD":[66],"extends":[68],"capabilities":[70,153],"our":[72],"previous":[73],"package,":[74],"Tools,":[76],"analyzing":[78],"performed":[81],"force":[85],"field.":[86],"GUI":[89,117,143,165],"features":[90],"an":[91],"intuitive":[92],"specialized":[95],"tabs":[96],"encompass":[98],"several":[99],"analyses":[100],"extract":[102],"data":[103],"from":[104],"trajectories.":[106],"In":[107],"this":[108],"work,":[109],"introduce":[111],"functionalities":[113],"through":[118],"two":[119],"case":[120],"studies":[121],"employing":[122],"MD":[124,157],"nucleosome":[128],"core":[129],"particle":[130],"(NCP)":[131],"membrane":[134],"bilayer.":[135],"By":[136],"providing":[137],"user-friendly":[139],"platform,":[140],"significantly":[144],"facilitates":[145],"simulation":[147],"while":[149],"expanding":[150],"analytical":[152],"available":[154,168],"community.":[158],"source":[160],"code":[161],"is":[166],"freely":[167],"at":[169],"https://github.com/SIRAHFF/SIRAH-Tools-GUI.":[170]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
