{"id":"https://openalex.org/W4360600105","doi":"https://doi.org/10.1186/s12859-023-05234-y","title":"Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS","display_name":"Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS","publication_year":2023,"publication_date":"2023-03-22","ids":{"openalex":"https://openalex.org/W4360600105","doi":"https://doi.org/10.1186/s12859-023-05234-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/36949402"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05234-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05234-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05234-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05234-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060349611","display_name":"Ivo Henrique Provensi Vieira","orcid":null},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"Ivo Henrique Provensi Vieira","raw_affiliation_strings":["Laborat\u00f3rio de Bioinform\u00e1tica e Qu\u00edmica Medicinal (LABIOQUIM), Funda\u00e7\u00e3o Oswaldo Cruz Rond\u00f4nia, Porto Velho, RO, Brasil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio de Bioinform\u00e1tica e Qu\u00edmica Medicinal (LABIOQUIM), Funda\u00e7\u00e3o Oswaldo Cruz Rond\u00f4nia, Porto Velho, RO, Brasil","institution_ids":["https://openalex.org/I52325"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049037395","display_name":"Eduardo Buganemi Botelho","orcid":null},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"Eduardo Buganemi Botelho","raw_affiliation_strings":["Laborat\u00f3rio de Bioinform\u00e1tica e Qu\u00edmica Medicinal (LABIOQUIM), Funda\u00e7\u00e3o Oswaldo Cruz Rond\u00f4nia, Porto Velho, RO, Brasil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio de Bioinform\u00e1tica e Qu\u00edmica Medicinal (LABIOQUIM), Funda\u00e7\u00e3o Oswaldo Cruz Rond\u00f4nia, Porto Velho, RO, Brasil","institution_ids":["https://openalex.org/I52325"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086846503","display_name":"Thales Junior de Souza Gomes","orcid":null},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"Thales Junior de Souza Gomes","raw_affiliation_strings":["Laborat\u00f3rio de Bioinform\u00e1tica e Qu\u00edmica Medicinal (LABIOQUIM), Funda\u00e7\u00e3o Oswaldo Cruz Rond\u00f4nia, Porto Velho, RO, Brasil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio de Bioinform\u00e1tica e Qu\u00edmica Medicinal (LABIOQUIM), Funda\u00e7\u00e3o Oswaldo Cruz Rond\u00f4nia, Porto Velho, RO, Brasil","institution_ids":["https://openalex.org/I52325"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002665527","display_name":"Roger Kist","orcid":"https://orcid.org/0000-0001-7338-2431"},"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":"Roger Kist","raw_affiliation_strings":["Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA, Porto Alegre, RS, Brasil","Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre \u2013 UFCSPA, Porto Alegre, RS, Brasil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA, Porto Alegre, RS, Brasil","institution_ids":["https://openalex.org/I134363262"]},{"raw_affiliation_string":"Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre \u2013 UFCSPA, Porto Alegre, RS, Brasil","institution_ids":["https://openalex.org/I134363262"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087642409","display_name":"Rafael Andrade Caceres","orcid":"https://orcid.org/0000-0002-7752-975X"},"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":"Rafael Andrade Caceres","raw_affiliation_strings":["Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA, Porto Alegre, RS, Brasil","Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre \u2013 UFCSPA, Porto Alegre, RS, Brasil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA, Porto Alegre, RS, Brasil","institution_ids":["https://openalex.org/I134363262"]},{"raw_affiliation_string":"Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre \u2013 UFCSPA, Porto Alegre, RS, Brasil","institution_ids":["https://openalex.org/I134363262"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056553635","display_name":"Fernando Berton Zanchi","orcid":"https://orcid.org/0000-0003-3386-0069"},"institutions":[{"id":"https://openalex.org/I123001628","display_name":"Universidade Federal de Rond\u00f4nia","ror":"https://ror.org/02842cb31","country_code":"BR","type":"education","lineage":["https://openalex.org/I123001628"]},{"id":"https://openalex.org/I4210091526","display_name":"Departamento de Epidemiolog\u00eda","ror":"https://ror.org/00ceh5s45","country_code":"GT","type":"government","lineage":["https://openalex.org/I4210091526","https://openalex.org/I4210118249"]},{"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","GT"],"is_corresponding":true,"raw_author_name":"Fernando Berton Zanchi","raw_affiliation_strings":["FIOCRUZ Rond\u00f4nia, Porto Velho, RO, Brazil. fernando.zanchi@fiocruz.br","Instituto Nacional de Epidemiologia na Amaz\u00f4nia Ocidental - EPIAMO, Porto Velho, RO, Brasil. fernando.zanchi@fiocruz.br","Laborat\u00f3rio de Bioinform\u00e1tica e Qu\u00edmica Medicinal (LABIOQUIM), Funda\u00e7\u00e3o Oswaldo Cruz Rond\u00f4nia, Porto Velho, RO, Brasil. fernando.zanchi@fiocruz.br","Programa de Doutorado em Ci\u00eancias - Coopera\u00e7\u00e3o IOC/Fiocruz Rond\u00f4nia: Biologia Computacional e Sistemas (BCS), Porto Velho, RO, Brasil. fernando.zanchi@fiocruz.br","Programa de P\u00f3s-Gradua\u00e7\u00e3o em Biologia Experimental, Universidade Federal de Rond\u00f4nia (UNIR), Porto Velho, RO, Brasil. fernando.zanchi@fiocruz.br","FIOCRUZ Rond\u00f4nia, Porto Velho, RO, Brazil"],"raw_orcid":"https://orcid.org/0000-0003-3386-0069","affiliations":[{"raw_affiliation_string":"FIOCRUZ Rond\u00f4nia, Porto Velho, RO, Brazil. fernando.zanchi@fiocruz.br","institution_ids":["https://openalex.org/I123001628"]},{"raw_affiliation_string":"Instituto Nacional de Epidemiologia na Amaz\u00f4nia Ocidental - EPIAMO, Porto Velho, RO, Brasil. fernando.zanchi@fiocruz.br","institution_ids":["https://openalex.org/I4210091526"]},{"raw_affiliation_string":"Laborat\u00f3rio de Bioinform\u00e1tica e Qu\u00edmica Medicinal (LABIOQUIM), Funda\u00e7\u00e3o Oswaldo Cruz Rond\u00f4nia, Porto Velho, RO, Brasil. fernando.zanchi@fiocruz.br","institution_ids":["https://openalex.org/I52325"]},{"raw_affiliation_string":"Programa de Doutorado em Ci\u00eancias - Coopera\u00e7\u00e3o IOC/Fiocruz Rond\u00f4nia: Biologia Computacional e Sistemas (BCS), Porto Velho, RO, Brasil. fernando.zanchi@fiocruz.br","institution_ids":["https://openalex.org/I123001628"]},{"raw_affiliation_string":"Programa de P\u00f3s-Gradua\u00e7\u00e3o em Biologia Experimental, Universidade Federal de Rond\u00f4nia (UNIR), Porto Velho, RO, Brasil. fernando.zanchi@fiocruz.br","institution_ids":["https://openalex.org/I123001628"]},{"raw_affiliation_string":"FIOCRUZ Rond\u00f4nia, Porto Velho, RO, Brazil","institution_ids":["https://openalex.org/I123001628","https://openalex.org/I52325"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5056553635"],"corresponding_institution_ids":["https://openalex.org/I123001628","https://openalex.org/I4210091526","https://openalex.org/I52325"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":18.2353,"has_fulltext":true,"cited_by_count":123,"citation_normalized_percentile":{"value":0.99572739,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","issue":"1","first_page":"107","last_page":"107"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.5425000190734863,"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":0.5425000190734863,"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":0.04740000143647194,"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"}},{"id":"https://openalex.org/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.03350000083446503,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.6831565499305725},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.668954610824585},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6350065469741821},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4644593894481659},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.41480857133865356},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.32815656065940857},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3118855357170105},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2046336829662323},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.11955904960632324},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11536237597465515}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6831565499305725},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.668954610824585},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6350065469741821},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4644593894481659},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.41480857133865356},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.32815656065940857},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3118855357170105},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2046336829662323},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.11955904960632324},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11536237597465515},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","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":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-023-05234-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05234-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05234-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36949402","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36949402","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10031864","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10031864","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10031864/pdf/12859_2023_Article_5234.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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:arca.fiocruz.br:icict/70630","is_oa":true,"landing_page_url":"https://arca.fiocruz.br/handle/icict/70630","pdf_url":null,"source":{"id":"https://openalex.org/S7407055450","display_name":"Arca - Reposit\u00f3rio Institucional da Fiocruz","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:doaj.org/article:1b417199c11741ca9eaf3e0e8274238d","is_oa":true,"landing_page_url":"https://doaj.org/article/1b417199c11741ca9eaf3e0e8274238d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-8 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05234-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05234-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05234-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"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/F4320323917","display_name":"Funda\u00e7\u00e3o Oswaldo Cruz","ror":"https://ror.org/04jhswv08"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4360600105.pdf"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1607931568","https://openalex.org/W1964831810","https://openalex.org/W1978159078","https://openalex.org/W1981021420","https://openalex.org/W1993299482","https://openalex.org/W2015642465","https://openalex.org/W2029667189","https://openalex.org/W2045683699","https://openalex.org/W2053538195","https://openalex.org/W2093381148","https://openalex.org/W2101078720","https://openalex.org/W2105668062","https://openalex.org/W2114367386","https://openalex.org/W2118200955","https://openalex.org/W2127522551","https://openalex.org/W2127821584","https://openalex.org/W2131736388","https://openalex.org/W2132629607","https://openalex.org/W2397547384","https://openalex.org/W2485899394","https://openalex.org/W2572080171","https://openalex.org/W3043252841","https://openalex.org/W4230842383"],"related_works":["https://openalex.org/W2023156907","https://openalex.org/W3094899115","https://openalex.org/W1968806281","https://openalex.org/W3095515585","https://openalex.org/W4315498887","https://openalex.org/W4378377190","https://openalex.org/W4401585471","https://openalex.org/W2360970307","https://openalex.org/W2888679374","https://openalex.org/W1773535258"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,16,161],"molecular":[2,17,73,130],"dynamics":[3,18,74,131],"is":[4,117,138,151,163],"an":[5],"approach":[6],"to":[7,60,71],"obtain":[8],"kinetic":[9],"and":[10,34,106,124,155],"thermodynamic":[11],"characteristics":[12],"of":[13,26,88,112,129],"biomolecular":[14],"structures.":[15],"simulation":[19,75,87],"softwares":[20],"are":[21,28,46],"very":[22],"useful,":[23],"however,":[24],"most":[25],"them":[27],"used":[29],"in":[30,65,91,126],"command":[31],"line":[32],"form":[33,94],"continue":[35],"with":[36,97,148],"the":[37,55,82,89,92,103,110,113,127],"same":[38],"common":[39],"implementation":[40],"difficulties":[41],"that":[42,120],"plague":[43],"researchers":[44],"who":[45],"not":[47],"computer":[48],"specialists.":[49],"RESULTS:":[50],"Here,":[51],"we":[52],"have":[53],"developed":[54,59,147],"VisualDynamics-a":[56],"WEB":[57],"tool":[58,119],"automate":[61],"biological":[62],"simulations":[63],"performed":[64],"Gromacs":[66],"using":[67],"a":[68,86,98,118,152],"graphical":[69],"interface":[70],"make":[72],"user-friendly":[76],"task.":[77],"In":[78],"this":[79],"new":[80],"application":[81],"researcher":[83],"can":[84],"submit":[85],"protein":[90],"free":[93,154],"or":[95],"complexed":[96],"ligand.":[99],"Can":[100],"also":[101],"download":[102,167],"graphics":[104],"analysis":[105],"log":[107],"files":[108],"at":[109,135,168],"end":[111],"simulation.":[114,132],"CONCLUSIONS:":[115],"VisualDynamics":[116,145],"will":[121],"accelerate":[122],"implementations":[123],"learning":[125],"area":[128],"Freely":[133],"available":[134,165],"https://visualdynamics.fiocruz.br/login":[136],",":[137],"supported":[139],"by":[140],"all":[141],"major":[142],"web":[143,159],"browsers.":[144],"was":[146],"Flask,":[149],"which":[150],"Python-based":[153],"open-source":[156],"framework":[157],"for":[158,166],"development.":[160],"code":[162],"freely":[164],"GitHub":[169],"https://github.com/LABIOQUIM/visualdynamics":[170],".":[171]},"counts_by_year":[{"year":2026,"cited_by_count":21},{"year":2025,"cited_by_count":66},{"year":2024,"cited_by_count":28},{"year":2023,"cited_by_count":8}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
