{"id":"https://openalex.org/W1989904188","doi":"https://doi.org/10.1371/journal.pcbi.1003719","title":"Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial","display_name":"Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial","publication_year":2014,"publication_date":"2014-07-24","ids":{"openalex":"https://openalex.org/W1989904188","doi":"https://doi.org/10.1371/journal.pcbi.1003719","mag":"1989904188","pmid":"https://pubmed.ncbi.nlm.nih.gov/25057988"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003719","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003719","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003719&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003719&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042039948","display_name":"Benjamin T. Miller","orcid":"https://orcid.org/0000-0002-2745-7794"},"institutions":[{"id":"https://openalex.org/I4210106489","display_name":"National Heart Lung and Blood Institute","ror":"https://ror.org/012pb6c26","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210106489"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Benjamin T. Miller","raw_affiliation_strings":["Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210106489"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085213833","display_name":"Rishi P. Singh","orcid":"https://orcid.org/0000-0001-5859-8162"},"institutions":[{"id":"https://openalex.org/I4210106489","display_name":"National Heart Lung and Blood Institute","ror":"https://ror.org/012pb6c26","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210106489"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rishi P. Singh","raw_affiliation_strings":["Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210106489"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074277733","display_name":"Vinushka Schalk","orcid":null},"institutions":[{"id":"https://openalex.org/I4056153","display_name":"New College of Florida","ror":"https://ror.org/01cbya385","country_code":"US","type":"education","lineage":["https://openalex.org/I4056153"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vinushka Schalk","raw_affiliation_strings":["Department of Natural Sciences, New College of Florida, Sarasota, Florida, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Natural Sciences, New College of Florida, Sarasota, Florida, United States of America","institution_ids":["https://openalex.org/I4056153"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075227698","display_name":"Yuri Pevzner","orcid":"https://orcid.org/0000-0002-6274-8765"},"institutions":[{"id":"https://openalex.org/I2613432","display_name":"University of South Florida","ror":"https://ror.org/032db5x82","country_code":"US","type":"education","lineage":["https://openalex.org/I2613432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuri Pevzner","raw_affiliation_strings":["Department of Chemistry, University of South Florida, Tampa, Florida, United States of America","Department of Chemistry , University of South Florida , Tampa , Florida , United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of South Florida, Tampa, Florida, United States of America","institution_ids":["https://openalex.org/I2613432"]},{"raw_affiliation_string":"Department of Chemistry , University of South Florida , Tampa , Florida , United States of America","institution_ids":["https://openalex.org/I2613432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045975465","display_name":"Jingjun Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I4210106489","display_name":"National Heart Lung and Blood Institute","ror":"https://ror.org/012pb6c26","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210106489"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jingjun Sun","raw_affiliation_strings":["Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210106489"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038962126","display_name":"Carrie S. Miller","orcid":"https://orcid.org/0000-0003-0990-4383"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carrie S. Miller","raw_affiliation_strings":["Department of Chemistry, Georgetown University, Washington, D.C., United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Georgetown University, Washington, D.C., United States of America","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042360417","display_name":"Stefan Boresch","orcid":"https://orcid.org/0000-0002-2793-6656"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Stefan Boresch","raw_affiliation_strings":["Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047602027","display_name":"Toshiko Ichiye","orcid":"https://orcid.org/0000-0003-2474-5253"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Toshiko Ichiye","raw_affiliation_strings":["Department of Chemistry, Georgetown University, Washington, D.C., United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Georgetown University, Washington, D.C., United States of America","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079782789","display_name":"Bernard R. Brooks","orcid":"https://orcid.org/0000-0002-3586-2730"},"institutions":[{"id":"https://openalex.org/I4210106489","display_name":"National Heart Lung and Blood Institute","ror":"https://ror.org/012pb6c26","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210106489"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bernard R. Brooks","raw_affiliation_strings":["Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210106489"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037901921","display_name":"H. Lee Woodcock","orcid":"https://orcid.org/0000-0003-3539-273X"},"institutions":[{"id":"https://openalex.org/I2613432","display_name":"University of South Florida","ror":"https://ror.org/032db5x82","country_code":"US","type":"education","lineage":["https://openalex.org/I2613432"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"H. Lee Woodcock","raw_affiliation_strings":["Department of Chemistry, University of South Florida, Tampa, Florida, United States of America","Department of Chemistry , University of South Florida , Tampa , Florida , United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of South Florida, Tampa, Florida, United States of America","institution_ids":["https://openalex.org/I2613432"]},{"raw_affiliation_string":"Department of Chemistry , University of South Florida , Tampa , Florida , United States of America","institution_ids":["https://openalex.org/I2613432"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5037901921","https://openalex.org/A5042039948"],"corresponding_institution_ids":["https://openalex.org/I2613432","https://openalex.org/I4210106489"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.1409,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.76698248,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"10","issue":"7","first_page":"e1003719","last_page":"e1003719"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.991100013256073,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.991100013256073,"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/T10412","display_name":"Microfluidic and Capillary Electrophoresis Applications","score":0.9853000044822693,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9830999970436096,"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/computer-science","display_name":"Computer science","score":0.7610349655151367},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.6955836415290833},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.662676215171814},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.5999001860618591},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.5566095113754272},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5247554779052734},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.5069675445556641},{"id":"https://openalex.org/keywords/coursework","display_name":"Coursework","score":0.49487799406051636},{"id":"https://openalex.org/keywords/web-based-simulation","display_name":"Web-based simulation","score":0.47621116042137146},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics","score":0.4699041247367859},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.45744606852531433},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4512809216976166},{"id":"https://openalex.org/keywords/multimedia","display_name":"Multimedia","score":0.3728639483451843},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.33546268939971924},{"id":"https://openalex.org/keywords/web-development","display_name":"Web development","score":0.3335267901420593},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.2993391752243042},{"id":"https://openalex.org/keywords/web-api","display_name":"Web API","score":0.22216752171516418},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.20363885164260864},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.18979501724243164},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1006421148777008}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7610349655151367},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.6955836415290833},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.662676215171814},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.5999001860618591},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.5566095113754272},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5247554779052734},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.5069675445556641},{"id":"https://openalex.org/C2781110425","wikidata":"https://www.wikidata.org/wiki/Q2074695","display_name":"Coursework","level":2,"score":0.49487799406051636},{"id":"https://openalex.org/C154314014","wikidata":"https://www.wikidata.org/wiki/Q7978411","display_name":"Web-based simulation","level":5,"score":0.47621116042137146},{"id":"https://openalex.org/C77660652","wikidata":"https://www.wikidata.org/wiki/Q150971","display_name":"Computer graphics","level":2,"score":0.4699041247367859},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.45744606852531433},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4512809216976166},{"id":"https://openalex.org/C49774154","wikidata":"https://www.wikidata.org/wiki/Q131765","display_name":"Multimedia","level":1,"score":0.3728639483451843},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.33546268939971924},{"id":"https://openalex.org/C79373723","wikidata":"https://www.wikidata.org/wiki/Q386275","display_name":"Web development","level":3,"score":0.3335267901420593},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.2993391752243042},{"id":"https://openalex.org/C127613066","wikidata":"https://www.wikidata.org/wiki/Q557770","display_name":"Web API","level":4,"score":0.22216752171516418},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.20363885164260864},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.18979501724243164},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1006421148777008},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C509550671","wikidata":"https://www.wikidata.org/wiki/Q126945","display_name":"Medical education","level":1,"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":"D003194","descriptor_name":"Computer-Assisted Instruction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003194","descriptor_name":"Computer-Assisted Instruction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003194","descriptor_name":"Computer-Assisted Instruction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":true},{"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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1003719","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003719","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003719&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:25057988","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25057988","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:digitalcommons.usf.edu:chm_facpub-1010","is_oa":true,"landing_page_url":"https://digitalcommons.usf.edu/chm_facpub/11","pdf_url":null,"source":{"id":"https://openalex.org/S4377196272","display_name":"Digital Commons - University of South Florida (University of South Florida)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2613432","host_organization_name":"University of South Florida","host_organization_lineage":["https://openalex.org/I2613432"],"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":"Chemistry Faculty Publications","raw_type":"article"},{"id":"pmh:oai:scholarcommons.usf.edu:chm_facpub-1010","is_oa":true,"landing_page_url":"https://scholarcommons.usf.edu/chm_facpub/11","pdf_url":null,"source":{"id":"https://openalex.org/S4377196272","display_name":"Digital Commons - University of South Florida (University of South Florida)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2613432","host_organization_name":"University of South Florida","host_organization_lineage":["https://openalex.org/I2613432"],"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":"Chemistry Faculty Publications","raw_type":"text"},{"id":"pmh:info:fedora/oai:univie.ac.at:o:467424","is_oa":true,"landing_page_url":"https://phaidra.univie.ac.at/o:467424","pdf_url":null,"source":{"id":"https://openalex.org/S4306401993","display_name":"Phaidra (Universit\u00e4t Wien)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I129774422","host_organization_name":"University of Vienna","host_organization_lineage":["https://openalex.org/I129774422"],"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":"ISSN:1553-7358","raw_type":"article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1003719","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003719","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:935989558a1943f4a9b1b42de82854d2","is_oa":true,"landing_page_url":"https://doaj.org/article/935989558a1943f4a9b1b42de82854d2","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 10, Iss 7, p e1003719 (2014)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3080938","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4109840","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003719","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003719","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003719&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6000000238418579,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G1197336449","display_name":"Theoretical Studies of the Cytosol","funder_award_id":"1158267","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2874873581","display_name":null,"funder_award_id":"CHE-1158267","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3876110867","display_name":null,"funder_award_id":"1K22HL088341-01A1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G561272332","display_name":null,"funder_award_id":"CHE-1158267","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G7169080348","display_name":null,"funder_award_id":"1K22HL088341-01A1","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G749854835","display_name":null,"funder_award_id":"08834","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310847","display_name":"University of South Florida","ror":"https://ror.org/032db5x82"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W1989904188.pdf"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W322962242","https://openalex.org/W1521042556","https://openalex.org/W1608369028","https://openalex.org/W1960408443","https://openalex.org/W1971456069","https://openalex.org/W1975769356","https://openalex.org/W1975945758","https://openalex.org/W1976096853","https://openalex.org/W1984367222","https://openalex.org/W1986193392","https://openalex.org/W1997772366","https://openalex.org/W1998107795","https://openalex.org/W2004303971","https://openalex.org/W2007961905","https://openalex.org/W2011703027","https://openalex.org/W2012345434","https://openalex.org/W2013979082","https://openalex.org/W2019701333","https://openalex.org/W2019893551","https://openalex.org/W2021520922","https://openalex.org/W2027815611","https://openalex.org/W2028130802","https://openalex.org/W2029582401","https://openalex.org/W2029667189","https://openalex.org/W2030384127","https://openalex.org/W2030942416","https://openalex.org/W2031468878","https://openalex.org/W2035460800","https://openalex.org/W2035720425","https://openalex.org/W2039184796","https://openalex.org/W2039781258","https://openalex.org/W2041902442","https://openalex.org/W2049286183","https://openalex.org/W2060433756","https://openalex.org/W2066414494","https://openalex.org/W2067174909","https://openalex.org/W2070753604","https://openalex.org/W2096921126","https://openalex.org/W2106257360","https://openalex.org/W2110872379","https://openalex.org/W2112315506","https://openalex.org/W2120901082","https://openalex.org/W2129020329","https://openalex.org/W2130479394","https://openalex.org/W2132262459","https://openalex.org/W2141877184","https://openalex.org/W2154181301","https://openalex.org/W2156012420","https://openalex.org/W2156842609","https://openalex.org/W2163210644","https://openalex.org/W2188111603","https://openalex.org/W2316011606","https://openalex.org/W2502686540","https://openalex.org/W4254881066","https://openalex.org/W4290802914"],"related_works":["https://openalex.org/W3136060338","https://openalex.org/W2267593226","https://openalex.org/W1963685508","https://openalex.org/W641981999","https://openalex.org/W168259169","https://openalex.org/W2280266861","https://openalex.org/W2112243808","https://openalex.org/W2282189566","https://openalex.org/W3215563387","https://openalex.org/W2379737872"],"abstract_inverted_index":{"This":[0],"article":[1],"describes":[2],"the":[3,38,105,125,128,151,158],"development,":[4],"implementation,":[5],"and":[6,14,43,79,90,117,132,157],"use":[7],"of":[8,20,95,104],"web-based":[9,73,109],"\"lessons\"":[10],"to":[11,17,68,108,123,139,149,162],"introduce":[12],"students":[13],"other":[15],"newcomers":[16],"computer":[18],"simulations":[19,164],"biological":[21],"macromolecules.":[22],"These":[23],"lessons,":[24],"i.e.,":[25],"interactive":[26],"step-by-step":[27],"instructions":[28],"for":[29],"performing":[30],"common":[31],"molecular":[32],"simulation":[33,98,119,155],"tasks,":[34],"are":[35,80],"integrated":[36],"into":[37,100],"collaboratively":[39],"developed":[40,55,144],"CHARMM":[41],"INterface":[42],"Graphics":[44],"(CHARMMing)":[45],"web":[46,86],"user":[47,126,166],"interface":[48,167],"(http://www.charmming.org).":[49],"Several":[50],"lessons":[51,71],"have":[52,76,143],"already":[53],"been":[54,77,114],"with":[56,83],"new":[57,70],"ones":[58],"easily":[59],"added":[60],"via":[61],"a":[62,145],"provided":[63],"Python":[64],"script.":[65],"In":[66,137],"addition":[67],"CHARMMing's":[69],"functionality,":[72],"graphical":[74,154],"capabilities":[75],"overhauled":[78],"fully":[81],"compatible":[82],"modern":[84],"mobile":[85],"browsers":[87],"(e.g.,":[88],"phones":[89],"tablets),":[91],"allowing":[92],"easy":[93],"integration":[94],"these":[96],"advanced":[97],"techniques":[99],"coursework.":[101],"Finally,":[102],"one":[103],"primary":[106],"objections":[107],"systems":[110],"like":[111],"CHARMMing":[112],"has":[113],"that":[115],"\"point":[116],"click\"":[118],"set-up":[120],"does":[121],"little":[122],"teach":[124],"about":[127],"underlying":[129],"physics,":[130],"biology,":[131],"computational":[133],"methods":[134],"being":[135],"applied.":[136],"response":[138],"this":[140],"criticism,":[141],"we":[142],"freely":[146],"available":[147],"tutorial":[148],"bridge":[150],"gap":[152],"between":[153],"setup":[156],"technical":[159],"knowledge":[160],"necessary":[161],"perform":[163],"without":[165],"assistance.":[168]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}