{"id":"https://openalex.org/W4401745183","doi":"https://doi.org/10.3389/fbinf.2024.1353807","title":"Design principles for molecular animation","display_name":"Design principles for molecular animation","publication_year":2024,"publication_date":"2024-08-21","ids":{"openalex":"https://openalex.org/W4401745183","doi":"https://doi.org/10.3389/fbinf.2024.1353807","pmid":"https://pubmed.ncbi.nlm.nih.gov/39234148"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2024.1353807","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1353807","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1353807/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1353807/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055546884","display_name":"Stuart G Jantzen","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Stuart G. Jantzen","raw_affiliation_strings":["Biocinematics, Victoria, BC, Canada","Science Visualization Lab, Biomedical Communications, Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada"],"affiliations":[{"raw_affiliation_string":"Biocinematics, Victoria, BC, Canada","institution_ids":[]},{"raw_affiliation_string":"Science Visualization Lab, Biomedical Communications, Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080088481","display_name":"Ga\u00ebl McGill","orcid":"https://orcid.org/0000-0003-2264-0132"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210105544","display_name":"Digizyme (United States)","ror":"https://ror.org/01fx7cm24","country_code":"US","type":"company","lineage":["https://openalex.org/I4210105544"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ga\u00ebl McGill","raw_affiliation_strings":["Center for Molecular and Cellular Dynamics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States","Digizyme, Brookline, MA, United States"],"affiliations":[{"raw_affiliation_string":"Center for Molecular and Cellular Dynamics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Digizyme, Brookline, MA, United States","institution_ids":["https://openalex.org/I4210105544"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065018982","display_name":"Jodie Jenkinson","orcid":"https://orcid.org/0000-0002-4066-9732"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Jodie Jenkinson","raw_affiliation_strings":["Science Visualization Lab, Biomedical Communications, Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada"],"affiliations":[{"raw_affiliation_string":"Science Visualization Lab, Biomedical Communications, Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065018982"],"corresponding_institution_ids":["https://openalex.org/I185261750"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.2361,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.57040328,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"4","issue":null,"first_page":"1353807","last_page":"1353807"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9696000218391418,"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":0.9696000218391418,"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/T12327","display_name":"Various Chemistry Research Topics","score":0.9248999953269958,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/animation","display_name":"Animation","score":0.7180884480476379},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.6098949909210205},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6089445352554321},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.605236828327179},{"id":"https://openalex.org/keywords/agency","display_name":"Agency (philosophy)","score":0.5792356133460999},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5699865818023682},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5536947846412659},{"id":"https://openalex.org/keywords/design-elements-and-principles","display_name":"Design elements and principles","score":0.5061807036399841},{"id":"https://openalex.org/keywords/molecular-graphics","display_name":"Molecular graphics","score":0.47010037302970886},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.4632697105407715},{"id":"https://openalex.org/keywords/motion","display_name":"Motion (physics)","score":0.4173990488052368},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.37109100818634033},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.32520025968551636},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics","score":0.2768632769584656},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.1639968454837799},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13150125741958618},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.11781144142150879},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08247581124305725}],"concepts":[{"id":"https://openalex.org/C502989409","wikidata":"https://www.wikidata.org/wiki/Q11425","display_name":"Animation","level":2,"score":0.7180884480476379},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.6098949909210205},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6089445352554321},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.605236828327179},{"id":"https://openalex.org/C108170787","wikidata":"https://www.wikidata.org/wiki/Q3951828","display_name":"Agency (philosophy)","level":2,"score":0.5792356133460999},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5699865818023682},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5536947846412659},{"id":"https://openalex.org/C33276779","wikidata":"https://www.wikidata.org/wiki/Q1943363","display_name":"Design elements and principles","level":2,"score":0.5061807036399841},{"id":"https://openalex.org/C126766683","wikidata":"https://www.wikidata.org/wiki/Q6896006","display_name":"Molecular graphics","level":3,"score":0.47010037302970886},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.4632697105407715},{"id":"https://openalex.org/C104114177","wikidata":"https://www.wikidata.org/wiki/Q79782","display_name":"Motion (physics)","level":2,"score":0.4173990488052368},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.37109100818634033},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.32520025968551636},{"id":"https://openalex.org/C77660652","wikidata":"https://www.wikidata.org/wiki/Q150971","display_name":"Computer graphics","level":2,"score":0.2768632769584656},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.1639968454837799},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13150125741958618},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.11781144142150879},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08247581124305725},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2024.1353807","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1353807","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1353807/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39234148","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39234148","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11371733","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11371733","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11371733/pdf/fbinf-04-1353807.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:37a3f936f8584d8e960c5369e091e511","is_oa":true,"landing_page_url":"https://doaj.org/article/37a3f936f8584d8e960c5369e091e511","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 4 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2024.1353807","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1353807","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1353807/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6600000262260437,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G2142912125","display_name":"The Vernon lyrics: texts and contexts","funder_award_id":"20512","funder_id":"https://openalex.org/F4320334617","funder_display_name":"Social Sciences and Humanities Research Council of Canada"},{"id":"https://openalex.org/G2401062268","display_name":null,"funder_award_id":"SIG-13/14","funder_id":"https://openalex.org/F4320334617","funder_display_name":"Social Sciences and Humanities Research Council of Canada"},{"id":"https://openalex.org/G4446706370","display_name":"Les femmes ministres dans le monde : qu'est-ce qui d\u00e9termine leur proportion","funder_award_id":"12205","funder_id":"https://openalex.org/F4320334617","funder_display_name":"Social Sciences and Humanities Research Council of Canada"},{"id":"https://openalex.org/G4824383381","display_name":"Visualizing Protein Interactions and Dynamics: Evolving a Visual Language to Support Learning in Undergraduate Science Education","funder_award_id":"1220512","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7838423458","display_name":"From bebop to hip hop:  towards a new theory of cultural innovation","funder_award_id":"22051","funder_id":"https://openalex.org/F4320334617","funder_display_name":"Social Sciences and Humanities Research Council of Canada"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320334617","display_name":"Social Sciences and Humanities Research Council of Canada","ror":"https://ror.org/04j5jqy92"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4401745183.pdf","grobid_xml":"https://content.openalex.org/works/W4401745183.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1489700509","https://openalex.org/W1518553298","https://openalex.org/W1909665669","https://openalex.org/W2052150953","https://openalex.org/W2066607505","https://openalex.org/W2108919989","https://openalex.org/W2111649842","https://openalex.org/W2113403117","https://openalex.org/W2125294256","https://openalex.org/W2131187223","https://openalex.org/W2140675067","https://openalex.org/W2144736543","https://openalex.org/W2145712327","https://openalex.org/W2293691271","https://openalex.org/W2315182751","https://openalex.org/W2318902520","https://openalex.org/W2549327495","https://openalex.org/W2615746795","https://openalex.org/W2888998702","https://openalex.org/W2912500398","https://openalex.org/W2957177175","https://openalex.org/W3023765427","https://openalex.org/W3086299328","https://openalex.org/W3089833548","https://openalex.org/W3166978960","https://openalex.org/W4206383980","https://openalex.org/W4225414631","https://openalex.org/W4280647514","https://openalex.org/W4283270255","https://openalex.org/W4382240185","https://openalex.org/W4388169051","https://openalex.org/W4401608320"],"related_works":["https://openalex.org/W4310844315","https://openalex.org/W2532377291","https://openalex.org/W2000013817","https://openalex.org/W2068608913","https://openalex.org/W4296190881","https://openalex.org/W3124914020","https://openalex.org/W2366362996","https://openalex.org/W2517624617","https://openalex.org/W2750714020","https://openalex.org/W1980956817"],"abstract_inverted_index":{"Molecular":[0],"visualization":[1,221],"is":[2,63],"a":[3,176],"powerful":[4],"way":[5],"to":[6,44,59,68,101,132,143,202,223],"represent":[7],"the":[8,21,41,106,150,183,187,191,216,227],"complex":[9],"structure":[10,48],"of":[11,23,47,111,139,152,178,195,209,230],"molecules":[12,73],"and":[13,33,39,49,53,70,82,88,109,113,193,219,225],"their":[14,24,77],"higher":[15],"order":[16],"assemblies,":[17],"as":[18,20],"well":[19,37],"dynamics":[22],"interactions.":[25],"Although":[26,199],"conventions":[27],"for":[28,105],"depicting":[29,186],"static":[30],"molecular":[31,61,102,114,125,136,164,179,231],"structures":[32],"complexes":[34],"are":[35,92,99,130,156],"now":[36],"established":[38],"guide":[40],"viewer's":[42],"attention":[43,52],"specific":[45],"aspects":[46],"function,":[50],"little":[51],"design":[54,96,119,127,197,210],"classification":[55],"has":[56],"been":[57],"devoted":[58],"how":[60,72],"motion":[62],"depicted.":[64],"As":[65],"we":[66,91,121,173,205],"continue":[67],"probe":[69],"discover":[71],"move":[74],"-":[75,90],"including":[76],"internal":[78],"flexibility,":[79],"conformational":[80],"changes":[81],"dynamic":[83],"associations":[84],"with":[85,94],"binding":[86],"partners":[87],"environments":[89],"faced":[93],"difficult":[95],"challenges":[97],"that":[98,129,145,166,181,196],"relevant":[100],"visualizations":[103],"both":[104],"scientific":[107,220],"community":[108],"students":[110,146],"cell":[112],"biology.":[115],"To":[116],"facilitate":[117,224],"these":[118,140],"decisions,":[120],"have":[122,147,174],"identified":[123],"twelve":[124],"animation":[126],"principles":[128,141,211],"important":[131],"consider":[133],"when":[134],"creating":[135],"animations.":[137],"Many":[138],"pertain":[142],"misconceptions":[144],"primarily":[148],"regarding":[149],"agency":[151],"molecules,":[153],"while":[154],"others":[155],"derived":[157],"from":[158],"visual":[159],"treatments":[160],"frequently":[161],"observed":[162],"in":[163,190],"animations":[165,180],"may":[167],"promote":[168],"misconceptions.":[169],"For":[170],"each":[171],"principle,":[172],"created":[175],"pair":[177],"exemplify":[182],"principle":[184],"by":[185,215],"same":[188],"content":[189],"presence":[192],"absence":[194],"approach.":[198],"not":[200],"intended":[201],"be":[203,213],"prescriptive,":[204],"hope":[206],"this":[207],"set":[208],"can":[212],"used":[214],"scientific,":[217],"education,":[218],"communities":[222],"improve":[226],"pedagogical":[228],"effectiveness":[229],"animation.":[232]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-25T14:56:36.534964","created_date":"2025-10-10T00:00:00"}
