{"id":"https://openalex.org/W4406275780","doi":"https://doi.org/10.1021/acs.jcim.4c01639","title":"PACKMOL-GUI: An All-In-One VMD Interface for Efficient Molecular Packing","display_name":"PACKMOL-GUI: An All-In-One VMD Interface for Efficient Molecular Packing","publication_year":2025,"publication_date":"2025-01-11","ids":{"openalex":"https://openalex.org/W4406275780","doi":"https://doi.org/10.1021/acs.jcim.4c01639","pmid":"https://pubmed.ncbi.nlm.nih.gov/39797794"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01639","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01639","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01639","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01639","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056580249","display_name":"Jian Huang","orcid":"https://orcid.org/0000-0002-1955-4316"},"institutions":[{"id":"https://openalex.org/I1336742384","display_name":"Children's National","ror":"https://ror.org/03wa2q724","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1336742384"]},{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]},{"id":"https://openalex.org/I4210100294","display_name":"Center for Children","ror":"https://ror.org/00m9f2x37","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210100294"]},{"id":"https://openalex.org/I4210113495","display_name":"Children's Hospital of Zhejiang University","ror":"https://ror.org/025fyfd20","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210113495"]},{"id":"https://openalex.org/I4210142358","display_name":"National Institute of Child Health","ror":"https://ror.org/049mgby18","country_code":"PK","type":"healthcare","lineage":["https://openalex.org/I4210142358"]},{"id":"https://openalex.org/I4210153519","display_name":"First Affiliated Hospital of Soochow University","ror":"https://ror.org/051jg5p78","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210153519"]}],"countries":["CN","PK","US"],"is_corresponding":false,"raw_author_name":"Jian Huang","raw_affiliation_strings":["National Clinical Research Center for Child Health, National Children\u2019s Regional Medical Center","Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province","Zhejiang University School of Medicine , Children\u2019s Hospital","Department of Radiation Oncology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China"],"raw_orcid":"https://orcid.org/0000-0002-1955-4316","affiliations":[{"raw_affiliation_string":"National Clinical Research Center for Child Health, National Children\u2019s Regional Medical Center","institution_ids":["https://openalex.org/I4210100294","https://openalex.org/I1336742384"]},{"raw_affiliation_string":"Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province","institution_ids":["https://openalex.org/I4210142358"]},{"raw_affiliation_string":"Zhejiang University School of Medicine , Children\u2019s Hospital","institution_ids":["https://openalex.org/I4210113495"]},{"raw_affiliation_string":"Department of Radiation Oncology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China","institution_ids":["https://openalex.org/I3923682","https://openalex.org/I4210153519"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101468248","display_name":"Chenchen Wu","orcid":"https://orcid.org/0000-0002-2489-7532"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]},{"id":"https://openalex.org/I4210113495","display_name":"Children's Hospital of Zhejiang University","ror":"https://ror.org/025fyfd20","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210113495"]},{"id":"https://openalex.org/I4210153519","display_name":"First Affiliated Hospital of Soochow University","ror":"https://ror.org/051jg5p78","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210153519"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenchen Wu","raw_affiliation_strings":["Department of Radiation Oncology","The First Affiliated Hospital of Soochow University","National Clinical Research Center for Child Health, National Children's Regional Medical Center, Zhejiang University School of Medicine , Children's Hospital, Hangzhou 310052, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Radiation Oncology","institution_ids":[]},{"raw_affiliation_string":"The First Affiliated Hospital of Soochow University","institution_ids":["https://openalex.org/I3923682","https://openalex.org/I4210153519"]},{"raw_affiliation_string":"National Clinical Research Center for Child Health, National Children's Regional Medical Center, Zhejiang University School of Medicine , Children's Hospital, Hangzhou 310052, China","institution_ids":["https://openalex.org/I4210113495"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113241524","display_name":"Xiner Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiner Yang","raw_affiliation_strings":["Soochow University","State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions","State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Soochow University","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071784754","display_name":"Zaixing Yang","orcid":"https://orcid.org/0000-0003-3521-6867"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zaixing Yang","raw_affiliation_strings":["Soochow University","State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions","State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China"],"raw_orcid":"https://orcid.org/0000-0003-3521-6867","affiliations":[{"raw_affiliation_string":"Soochow University","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082491143","display_name":"Shengtang Liu","orcid":"https://orcid.org/0000-0001-9632-9377"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shengtang Liu","raw_affiliation_strings":["Soochow University","State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions","State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China"],"raw_orcid":"https://orcid.org/0000-0001-9632-9377","affiliations":[{"raw_affiliation_string":"Soochow University","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014738611","display_name":"Gang Yu","orcid":"https://orcid.org/0000-0001-9935-9969"},"institutions":[{"id":"https://openalex.org/I1336742384","display_name":"Children's National","ror":"https://ror.org/03wa2q724","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1336742384"]},{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]},{"id":"https://openalex.org/I4210100294","display_name":"Center for Children","ror":"https://ror.org/00m9f2x37","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210100294"]},{"id":"https://openalex.org/I4210113495","display_name":"Children's Hospital of Zhejiang University","ror":"https://ror.org/025fyfd20","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210113495"]},{"id":"https://openalex.org/I4210142358","display_name":"National Institute of Child Health","ror":"https://ror.org/049mgby18","country_code":"PK","type":"healthcare","lineage":["https://openalex.org/I4210142358"]},{"id":"https://openalex.org/I4210153519","display_name":"First Affiliated Hospital of Soochow University","ror":"https://ror.org/051jg5p78","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210153519"]}],"countries":["CN","PK","US"],"is_corresponding":true,"raw_author_name":"Gang Yu","raw_affiliation_strings":["National Clinical Research Center for Child Health, National Children\u2019s Regional Medical Center","Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province","Zhejiang University School of Medicine , Children\u2019s Hospital","Department of Radiation Oncology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China","Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province, Hangzhou 310052, China"],"raw_orcid":"https://orcid.org/0000-0001-9935-9969","affiliations":[{"raw_affiliation_string":"National Clinical Research Center for Child Health, National Children\u2019s Regional Medical Center","institution_ids":["https://openalex.org/I4210100294","https://openalex.org/I1336742384"]},{"raw_affiliation_string":"Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province","institution_ids":["https://openalex.org/I4210142358"]},{"raw_affiliation_string":"Zhejiang University School of Medicine , Children\u2019s Hospital","institution_ids":["https://openalex.org/I4210113495"]},{"raw_affiliation_string":"Department of Radiation Oncology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China","institution_ids":["https://openalex.org/I3923682","https://openalex.org/I4210153519"]},{"raw_affiliation_string":"Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province, Hangzhou 310052, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5014738611","https://openalex.org/A5082491143"],"corresponding_institution_ids":["https://openalex.org/I1336742384","https://openalex.org/I3923682","https://openalex.org/I4210100294","https://openalex.org/I4210113495","https://openalex.org/I4210142358","https://openalex.org/I4210153519"],"apc_list":null,"apc_paid":null,"fwci":4.2783,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.94422976,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"65","issue":"2","first_page":"778","last_page":"784"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9987000226974487,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9980000257492065,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.8264890909194946},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.8138527870178223},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7912617921829224},{"id":"https://openalex.org/keywords/extensibility","display_name":"Extensibility","score":0.7630741596221924},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7235506772994995},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6143741011619568},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5212324857711792},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.5139612555503845},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.44337233901023865},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.43251487612724304},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4243810176849365},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.410754919052124},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3052491843700409},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.16660532355308533},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.15956789255142212}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.8264890909194946},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.8138527870178223},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7912617921829224},{"id":"https://openalex.org/C32833848","wikidata":"https://www.wikidata.org/wiki/Q4115054","display_name":"Extensibility","level":2,"score":0.7630741596221924},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7235506772994995},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6143741011619568},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5212324857711792},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.5139612555503845},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.44337233901023865},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.43251487612724304},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4243810176849365},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.410754919052124},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3052491843700409},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.16660532355308533},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.15956789255142212},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"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":"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":"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":"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":"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":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","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":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.4c01639","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01639","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01639","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:39797794","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39797794","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:11776922","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11776922/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11776922/pdf/ci4c01639.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-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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.4c01639","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01639","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01639","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.5799999833106995}],"awards":[{"id":"https://openalex.org/G1565819666","display_name":null,"funder_award_id":"22106114","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2229497552","display_name":null,"funder_award_id":"62076218","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G2634417637","display_name":null,"funder_award_id":"22176137","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3205407076","display_name":null,"funder_award_id":"2023YFC2706400","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G5111979006","display_name":null,"funder_award_id":"62076218","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320327518","display_name":"Priority Academic Program Development of Jiangsu Higher Education Institutions","ror":null},{"id":"https://openalex.org/F4320330486","display_name":"State Key Laboratory of Radiation Medicine and Protection","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406275780.pdf","grobid_xml":"https://content.openalex.org/works/W4406275780.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1962871751","https://openalex.org/W1963883777","https://openalex.org/W1990771438","https://openalex.org/W2003949305","https://openalex.org/W2021200484","https://openalex.org/W2021520922","https://openalex.org/W2029667189","https://openalex.org/W2067263573","https://openalex.org/W2132262459","https://openalex.org/W2134762386","https://openalex.org/W2147050567","https://openalex.org/W2169678694","https://openalex.org/W2206954826","https://openalex.org/W2408504433","https://openalex.org/W2981507824","https://openalex.org/W2982049929","https://openalex.org/W3087236414","https://openalex.org/W3097493941","https://openalex.org/W4283374866","https://openalex.org/W4296824339","https://openalex.org/W4385334631"],"related_works":["https://openalex.org/W3022321974","https://openalex.org/W4386041260","https://openalex.org/W4298269242","https://openalex.org/W4298401663","https://openalex.org/W2129419898","https://openalex.org/W4300787769","https://openalex.org/W4302475558","https://openalex.org/W4301355831","https://openalex.org/W4298345637","https://openalex.org/W2170060741"],"abstract_inverted_index":{"PACKMOL":[0,71,107],"is":[1],"a":[2,25,52],"widely":[3],"utilized":[4],"molecular":[5,40,84,120],"modeling":[6],"tool":[7],"within":[8],"the":[9,21,37,57,61,67,81,97,104,116],"computational":[10],"chemistry":[11],"community.":[12],"However,":[13],"its":[14],"tremendous":[15],"advantages":[16],"have":[17,49],"been":[18],"impeded":[19],"by":[20],"longstanding":[22],"lack":[23],"of":[24,39,60,69,83,118],"robust":[26],"open-source":[27],"graphical":[28],"user":[29,76],"interface":[30],"(GUI)":[31],"that":[32,55],"integrates":[33],"parameter":[34],"settings":[35],"with":[36],"visualization":[38,82],"and":[41,86,92,106,111],"geometric":[42,87],"constraints.":[43],"To":[44],"address":[45],"this":[46],"limitation,":[47],"we":[48],"developed":[50],"PACKMOL-GUI,":[51],"VMD":[53,98,105],"plugin":[54],"leverages":[56],"dynamic":[58],"extensibility":[59],"Tcl/Tk":[62],"toolkit.":[63],"This":[64],"GUI":[65],"enables":[66],"configuration":[68],"all":[70],"parameters":[72],"through":[73],"an":[74,109],"intuitive":[75,110],"panel,":[77],"while":[78],"also":[79],"facilitating":[80],"structures":[85],"constraints,":[88],"including":[89],"cubes,":[90],"boxes,":[91],"spheres,":[93],"among":[94],"others":[95],"via":[96],"software.":[99],"The":[100],"seamless":[101],"interaction":[102],"between":[103],"provides":[108],"efficient":[112],"all-in-one":[113],"platform":[114],"for":[115],"packing":[117],"complex":[119],"systems.":[121]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":3}],"updated_date":"2026-07-20T07:56:41.581041","created_date":"2025-10-10T00:00:00"}