{"id":"https://openalex.org/W2981507824","doi":"https://doi.org/10.1021/acs.jcim.9b00739","title":"VMD Store\u2013A VMD Plugin to Browse, Discover, and Install VMD Extensions","display_name":"VMD Store\u2013A VMD Plugin to Browse, Discover, and Install VMD Extensions","publication_year":2019,"publication_date":"2019-10-21","ids":{"openalex":"https://openalex.org/W2981507824","doi":"https://doi.org/10.1021/acs.jcim.9b00739","mag":"2981507824","pmid":"https://pubmed.ncbi.nlm.nih.gov/31682440"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00739","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00739","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/A5084517680","display_name":"Henrique S. Fernandes","orcid":"https://orcid.org/0000-0002-9280-1838"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210138594","display_name":"Rede de Qu\u00edmica e Tecnologia","ror":"https://ror.org/04j14t006","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210138594"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Henrique S. Fernandes","raw_affiliation_strings":["UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hern\u00e2ni Monteiro, 4200-319 Porto, Portugal"],"raw_orcid":"https://orcid.org/0000-0002-9280-1838","affiliations":[{"raw_affiliation_string":"UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hern\u00e2ni Monteiro, 4200-319 Porto, Portugal","institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4210138594"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014536242","display_name":"S\u00e9rgio F. Sousa","orcid":null},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210138594","display_name":"Rede de Qu\u00edmica e Tecnologia","ror":"https://ror.org/04j14t006","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210138594"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"S\u00e9rgio F. Sousa","raw_affiliation_strings":["UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hern\u00e2ni Monteiro, 4200-319 Porto, Portugal"],"raw_orcid":"https://orcid.org/0000-0002-6560-5284","affiliations":[{"raw_affiliation_string":"UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hern\u00e2ni Monteiro, 4200-319 Porto, Portugal","institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4210138594"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009395701","display_name":"Nuno M. F. S. A. Cerqueira","orcid":"https://orcid.org/0000-0003-0342-7424"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210138594","display_name":"Rede de Qu\u00edmica e Tecnologia","ror":"https://ror.org/04j14t006","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210138594"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Nuno M. F. S. A. Cerqueira","raw_affiliation_strings":["UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hern\u00e2ni Monteiro, 4200-319 Porto, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hern\u00e2ni Monteiro, 4200-319 Porto, Portugal","institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4210138594"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5009395701"],"corresponding_institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4210138594"],"apc_list":null,"apc_paid":null,"fwci":1.5184,"has_fulltext":false,"cited_by_count":114,"citation_normalized_percentile":{"value":0.83122415,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"59","issue":"11","first_page":"4519","last_page":"4523"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9979000091552734,"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":0.9979000091552734,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9929999709129333,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9871000051498413,"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/plug-in","display_name":"Plug-in","score":0.9414156675338745},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6955690979957581},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.6502872705459595},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5782926082611084},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.43642759323120117},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.34102463722229004}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.9414156675338745},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6955690979957581},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.6502872705459595},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5782926082611084},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.43642759323120117},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.34102463722229004}],"mesh":[{"descriptor_ui":"D000080486","descriptor_name":"Computational Chemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000080486","descriptor_name":"Computational Chemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000080486","descriptor_name":"Computational Chemistry","qualifier_ui":null,"qualifier_name":null,"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":2,"locations":[{"id":"doi:10.1021/acs.jcim.9b00739","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00739","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:31682440","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31682440","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":[{"id":"https://openalex.org/G2051857746","display_name":null,"funder_award_id":"SFRH/BD/115396/2016","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G2835248180","display_name":null,"funder_award_id":"NORTE-01-0145-FEDER000024","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G5976336732","display_name":null,"funder_award_id":"IF/01310/2013","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6751739791","display_name":null,"funder_award_id":"UID/MULTI/04378/2013.UID/MULTI/04378/2013","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G812551818","display_name":null,"funder_award_id":"POCI-01\u20130145- FEDER-007728","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1892158199","https://openalex.org/W1962871751","https://openalex.org/W2013836123","https://openalex.org/W2023608346","https://openalex.org/W2029667189","https://openalex.org/W2054706479","https://openalex.org/W2107278499","https://openalex.org/W2124026197","https://openalex.org/W2132609238","https://openalex.org/W2132629607","https://openalex.org/W2147050567","https://openalex.org/W2282942461","https://openalex.org/W2292169708","https://openalex.org/W2337812067","https://openalex.org/W2408504433","https://openalex.org/W2609246443","https://openalex.org/W2742985178","https://openalex.org/W2743019238","https://openalex.org/W2786758259","https://openalex.org/W2792058791","https://openalex.org/W2919482020"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W47352601","https://openalex.org/W2981957539","https://openalex.org/W4386041260","https://openalex.org/W4298269242","https://openalex.org/W4298401663","https://openalex.org/W4300787769","https://openalex.org/W4302475558","https://openalex.org/W4301355831","https://openalex.org/W4298345637"],"abstract_inverted_index":{"Herein":[0],"we":[1],"present":[2],"the":[3,12,24,37],"VMD":[4,8,31,39,53,64,71,87],"Store,":[5],"an":[6,59],"open-source":[7],"plugin":[9,56],"that":[10,14],"simplifies":[11],"way":[13],"users":[15],"browse,":[16],"discover,":[17],"install,":[18],"update,":[19],"and":[20,44,51,81,85],"uninstall":[21],"extensions":[22,40,65],"for":[23,78],"Visual":[25],"Molecular":[26],"Dynamics":[27],"(VMD)":[28],"software.":[29],"The":[30,70],"Store":[32,72],"obtains":[33],"data":[34],"about":[35],"all":[36,63],"indexed":[38],"hosted":[41],"on":[42],"GitHub":[43],"presents":[45],"a":[46,67],"one-click":[47],"mechanism":[48],"to":[49,61],"install":[50],"configure":[52],"extensions.":[54],"This":[55],"arises":[57],"in":[58],"attempt":[60],"aggregate":[62],"into":[66],"single":[68],"platform.":[69],"is":[73],"available,":[74],"free":[75],"of":[76],"charge,":[77],"Windows,":[79],"macOS,":[80],"Linux":[82],"at":[83],"https://biosim.pt/software/":[84],"requires":[86],"1.9.3":[88],"(or":[89],"later).":[90]},"counts_by_year":[{"year":2026,"cited_by_count":17},{"year":2025,"cited_by_count":33},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
