{"id":"https://openalex.org/W3200045630","doi":"https://doi.org/10.1021/acs.jcim.1c00743","title":"Assembly of Biomolecular Gigastructures and Visualization with the Vulkan Graphics API","display_name":"Assembly of Biomolecular Gigastructures and Visualization with the Vulkan Graphics API","publication_year":2021,"publication_date":"2021-09-16","ids":{"openalex":"https://openalex.org/W3200045630","doi":"https://doi.org/10.1021/acs.jcim.1c00743","mag":"3200045630","pmid":"https://pubmed.ncbi.nlm.nih.gov/34528431"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c00743","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00743","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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://doi.org/10.1021/acs.jcim.1c00743","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076456364","display_name":"Kornel Ozvoldik","orcid":"https://orcid.org/0000-0002-0501-3551"},"institutions":[{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Kornel Ozvoldik","raw_affiliation_strings":["Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Waehringerstr. 13A, 1090 Vienna, Austria","YASARA Biosciences GmbH, Wagramer Str. 25/3/45, 1220 Vienna, Austria"],"raw_orcid":"https://orcid.org/0000-0002-0501-3551","affiliations":[{"raw_affiliation_string":"Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Waehringerstr. 13A, 1090 Vienna, Austria","institution_ids":["https://openalex.org/I76134821"]},{"raw_affiliation_string":"YASARA Biosciences GmbH, Wagramer Str. 25/3/45, 1220 Vienna, Austria","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038910133","display_name":"Thomas Stockner","orcid":"https://orcid.org/0000-0002-7071-8283"},"institutions":[{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Thomas Stockner","raw_affiliation_strings":["Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Waehringerstr. 13A, 1090 Vienna, Austria"],"raw_orcid":"https://orcid.org/0000-0002-7071-8283","affiliations":[{"raw_affiliation_string":"Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Waehringerstr. 13A, 1090 Vienna, Austria","institution_ids":["https://openalex.org/I76134821"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036602771","display_name":"Burkhard Rammner","orcid":null},"institutions":[{"id":"https://openalex.org/I4210150726","display_name":"Plasmatreat (Germany)","ror":"https://ror.org/05cx80085","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210150726"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Burkhard Rammner","raw_affiliation_strings":["Sciloop, Karl-Theodor-Strasse 20, 22765 Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sciloop, Karl-Theodor-Strasse 20, 22765 Hamburg, Germany","institution_ids":["https://openalex.org/I4210150726"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027566465","display_name":"Elmar Krieger","orcid":"https://orcid.org/0000-0003-3010-2721"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Elmar Krieger","raw_affiliation_strings":["YASARA Biosciences GmbH, Wagramer Str. 25/3/45, 1220 Vienna, Austria"],"raw_orcid":"https://orcid.org/0000-0003-3010-2721","affiliations":[{"raw_affiliation_string":"YASARA Biosciences GmbH, Wagramer Str. 25/3/45, 1220 Vienna, Austria","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5027566465"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":5.2365,"has_fulltext":false,"cited_by_count":38,"citation_normalized_percentile":{"value":0.95831952,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"61","issue":"10","first_page":"5293","last_page":"5303"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9909999966621399,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9750000238418579,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7040407061576843},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6482287049293518},{"id":"https://openalex.org/keywords/molecular-graphics","display_name":"Molecular graphics","score":0.6138518452644348},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.5890895128250122},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.585049033164978},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics","score":0.4832066297531128},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.47411587834358215},{"id":"https://openalex.org/keywords/atom","display_name":"Atom (system on chip)","score":0.42820584774017334},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.42411336302757263},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1726316511631012},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.13276523351669312}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7040407061576843},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6482287049293518},{"id":"https://openalex.org/C126766683","wikidata":"https://www.wikidata.org/wiki/Q6896006","display_name":"Molecular graphics","level":3,"score":0.6138518452644348},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.5890895128250122},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.585049033164978},{"id":"https://openalex.org/C77660652","wikidata":"https://www.wikidata.org/wiki/Q150971","display_name":"Computer graphics","level":2,"score":0.4832066297531128},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.47411587834358215},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.42820584774017334},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.42411336302757263},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1726316511631012},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.13276523351669312},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":4,"locations":[{"id":"doi:10.1021/acs.jcim.1c00743","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00743","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:34528431","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34528431","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:europepmc.org:7438288","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8549067","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8549067","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8549067","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.1c00743","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00743","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2017672025","display_name":null,"funder_award_id":"860954","funder_id":"https://openalex.org/F4320338337","funder_display_name":"H2020 Marie Sk\u0142odowska-Curie Actions"},{"id":"https://openalex.org/G3134137401","display_name":null,"funder_award_id":"P32017","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"}],"funders":[{"id":"https://openalex.org/F4320321181","display_name":"Austrian Science Fund","ror":"https://ror.org/013tf3c58"},{"id":"https://openalex.org/F4320338337","display_name":"H2020 Marie Sk\u0142odowska-Curie Actions","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1963514652","https://openalex.org/W1973730326","https://openalex.org/W1974035453","https://openalex.org/W1984678540","https://openalex.org/W2056247431","https://openalex.org/W2067484689","https://openalex.org/W2069165179","https://openalex.org/W2099099776","https://openalex.org/W2119267663","https://openalex.org/W2120238752","https://openalex.org/W2152013121","https://openalex.org/W2154069299","https://openalex.org/W2154792548","https://openalex.org/W2162274915","https://openalex.org/W2229412420","https://openalex.org/W2291468715","https://openalex.org/W2404280981","https://openalex.org/W2581672095","https://openalex.org/W2751857862","https://openalex.org/W2753862885","https://openalex.org/W2798017727","https://openalex.org/W2910356247","https://openalex.org/W2949496165","https://openalex.org/W3013533831","https://openalex.org/W3027094385","https://openalex.org/W3083130172","https://openalex.org/W3103562591"],"related_works":["https://openalex.org/W2002869446","https://openalex.org/W2038255918","https://openalex.org/W2037810710","https://openalex.org/W1974904668","https://openalex.org/W2041985731","https://openalex.org/W200616046","https://openalex.org/W2051676847","https://openalex.org/W2018663386","https://openalex.org/W2475650533","https://openalex.org/W2412625894"],"abstract_inverted_index":{"Building":[0],"and":[1,36,96,136,187,210,219,248,273],"displaying":[2],"all-atom":[3,131,205],"models":[4,60,206],"of":[5,12,27,33,40,67,85,105,118,147,152,155,207,268],"biomolecular":[6,304],"structures":[7],"with":[8,48,69,89,99,138,163,215],"millions":[9],"or":[10,17],"billions":[11],"atoms,":[13,222],"like":[14],"virus":[15],"particles":[16],"cells,":[18],"remain":[19],"a":[20,164,171,200,297],"challenge":[21],"due":[22],"to":[23,56,129,133,174,195,227,241,251,256,286],"the":[24,28,30,37,49,71,83,86,92,116,130,143,150,237,253,269,288],"sheer":[25],"size":[26],"data,":[29],"required":[31],"levels":[32,154],"automated":[34],"building,":[35],"visualization":[38,146],"limits":[39],"today's":[41],"graphics":[42,182,239],"hardware.":[43],"Based":[44],"on":[45,244],"concepts":[46],"introduced":[47],"CellPack":[50],"program,":[51],"we":[52,203],"report":[53],"new":[54],"algorithms":[55],"create":[57,175],"such":[58,78,176,259],"large-scale":[59],"using":[61,223],"an":[62,211],"intermediate":[63],"coarse-grained":[64],"\"pet":[65],"representation\"":[66],"biomolecules":[68],"1/10th":[70],"normal":[72],"size.":[73],"Pet":[74],"atoms":[75],"are":[76,97,161],"placed":[77],"that":[79,189],"they":[80],"optimally":[81],"trace":[82],"surface":[84],"original":[87,93],"molecule":[88],"just":[90],"\u223c1/50th":[91],"atom":[94],"number":[95],"joined":[98],"covalent":[100],"bonds.":[101],"Molecular":[102],"dynamics":[103],"simulations":[104],"pet":[106,123],"molecules":[107,160,194],"allow":[108],"for":[109,142,178,301],"efficient":[110,144],"packing":[111],"optimization,":[112],"as":[113,115,266],"well":[114],"generation":[117],"realistic":[119],"DNA/RNA":[120],"conformations.":[121],"This":[122],"world":[124],"can":[125,283,292],"be":[126,134,284,293],"expanded":[127],"back":[128],"representation":[132],"explored":[135],"visualized":[137],"full":[139],"details.":[140],"Essential":[141],"interactive":[145],"gigastructures":[148],"is":[149,264],"use":[151,252],"multiple":[153],"detail":[156],"(LODs),":[157],"where":[158],"distant":[159],"drawn":[162],"heavily":[165],"reduced":[166],"polygon":[167],"count.":[168],"We":[169,235],"present":[170],"grid-based":[172],"algorithm":[173],"LODs":[177],"all":[179],"common":[180],"molecular":[181,271],"styles":[183],"(including":[184],"ball-and-sticks,":[185],"ribbons,":[186],"cartoons)":[188],"do":[190],"not":[191],"require":[192],"monochrome":[193],"hide":[196],"LOD":[197],"transitions.":[198],"As":[199],"practical":[201],"application,":[202],"built":[204],"SARS-CoV-2,":[208],"HIV,":[209],"entire":[212],"presynaptic":[213],"bouton":[214],"1":[216],"\u03bcm":[217],"diameter":[218],"3.6":[220],"billion":[221],"modular":[224],"building":[225],"blocks":[226],"significantly":[228],"reduce":[229],"GPU":[230],"memory":[231],"requirements":[232],"through":[233],"instancing.":[234],"employ":[236],"Vulkan":[238],"API":[240],"maximize":[242],"performance":[243],"consumer":[245],"grade":[246],"hardware":[247],"describe":[249],"how":[250],"mmCIF":[254],"format":[255],"efficiently":[257],"store":[258],"giant":[260,303],"models.":[261],"An":[262],"implementation":[263],"available":[265],"part":[267],"YASARA":[270,280],"modeling":[272],"simulation":[274],"program":[275,282],"from":[276,295],"www.YASARA.org.":[277],"The":[278],"free":[279],"View":[281],"used":[285],"explore":[287],"presented":[289],"models,":[290],"which":[291],"downloaded":[294],"www.YASARA.org/petworld,":[296],"Creative":[298],"Commons":[299],"platform":[300],"sharing":[302],"structures.":[305]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":5}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
