{"id":"https://openalex.org/W3200999538","doi":"https://doi.org/10.14529/jsfi210202","title":"Porting and Optimizing Molecular Docking onto the SX-Aurora TSUBASA Vector Computer","display_name":"Porting and Optimizing Molecular Docking onto the SX-Aurora TSUBASA Vector Computer","publication_year":2021,"publication_date":"2021-06-01","ids":{"openalex":"https://openalex.org/W3200999538","doi":"https://doi.org/10.14529/jsfi210202","mag":"3200999538"},"language":"en","primary_location":{"id":"doi:10.14529/jsfi210202","is_oa":true,"landing_page_url":"https://doi.org/10.14529/jsfi210202","pdf_url":"https://superfri.org/index.php/superfri/article/download/379/388","source":{"id":"https://openalex.org/S4210177204","display_name":"Supercomputing Frontiers and Innovations","issn_l":"2313-8734","issn":["2313-8734","2409-6008"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310312680","host_organization_name":"Publishing center of the South Ural State University","host_organization_lineage":["https://openalex.org/P4310312680"],"host_organization_lineage_names":["Publishing center of the South Ural State University"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Supercomputing Frontiers and Innovations","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://superfri.org/index.php/superfri/article/download/379/388","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037721262","display_name":"Leonardo Solis-Vasquez","orcid":"https://orcid.org/0000-0001-6896-9879"},"institutions":[{"id":"https://openalex.org/I31512782","display_name":"Technische Universit\u00e4t Darmstadt","ror":"https://ror.org/05n911h24","country_code":"DE","type":"education","lineage":["https://openalex.org/I31512782"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Leonardo Solis-Vasquez","raw_affiliation_strings":["Technical University of Darmstadt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Technical University of Darmstadt","institution_ids":["https://openalex.org/I31512782"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004513697","display_name":"Erich Focht","orcid":null},"institutions":[{"id":"https://openalex.org/I4210164122","display_name":"NEC (Germany)","ror":"https://ror.org/05hxss661","country_code":"DE","type":"company","lineage":["https://openalex.org/I118347220","https://openalex.org/I4210164122"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Erich Focht","raw_affiliation_strings":["NEC Deutschland GmbH"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NEC Deutschland GmbH","institution_ids":["https://openalex.org/I4210164122"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047000315","display_name":"Andreas Koch","orcid":"https://orcid.org/0000-0002-1164-3082"},"institutions":[{"id":"https://openalex.org/I31512782","display_name":"Technische Universit\u00e4t Darmstadt","ror":"https://ror.org/05n911h24","country_code":"DE","type":"education","lineage":["https://openalex.org/I31512782"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Koch","raw_affiliation_strings":["Technical University of Darmstadt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Technical University of Darmstadt","institution_ids":["https://openalex.org/I31512782"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0814,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.4463364,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"8","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12534","display_name":"Protein Degradation and Inhibitors","score":0.9990000128746033,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":0.9990000128746033,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9983000159263611,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9883999824523926,"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/porting","display_name":"Porting","score":0.919723391532898},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7174725532531738},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.6670017242431641},{"id":"https://openalex.org/keywords/autodock","display_name":"AutoDock","score":0.6499752998352051},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.4134944975376129},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.37975457310676575},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.37102270126342773},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2856959104537964},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.24470514059066772},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.14774563908576965}],"concepts":[{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.919723391532898},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7174725532531738},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6670017242431641},{"id":"https://openalex.org/C2780152424","wikidata":"https://www.wikidata.org/wiki/Q4826062","display_name":"AutoDock","level":4,"score":0.6499752998352051},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.4134944975376129},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.37975457310676575},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.37102270126342773},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2856959104537964},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.24470514059066772},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.14774563908576965},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.14529/jsfi210202","is_oa":true,"landing_page_url":"https://doi.org/10.14529/jsfi210202","pdf_url":"https://superfri.org/index.php/superfri/article/download/379/388","source":{"id":"https://openalex.org/S4210177204","display_name":"Supercomputing Frontiers and Innovations","issn_l":"2313-8734","issn":["2313-8734","2409-6008"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310312680","host_organization_name":"Publishing center of the South Ural State University","host_organization_lineage":["https://openalex.org/P4310312680"],"host_organization_lineage_names":["Publishing center of the South Ural State University"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Supercomputing Frontiers and Innovations","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.14529/jsfi210202","is_oa":true,"landing_page_url":"https://doi.org/10.14529/jsfi210202","pdf_url":"https://superfri.org/index.php/superfri/article/download/379/388","source":{"id":"https://openalex.org/S4210177204","display_name":"Supercomputing Frontiers and Innovations","issn_l":"2313-8734","issn":["2313-8734","2409-6008"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310312680","host_organization_name":"Publishing center of the South Ural State University","host_organization_lineage":["https://openalex.org/P4310312680"],"host_organization_lineage_names":["Publishing center of the South Ural State University"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Supercomputing Frontiers and Innovations","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5400000214576721}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3200999538.pdf","grobid_xml":"https://content.openalex.org/works/W3200999538.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W6908809","https://openalex.org/W780656674","https://openalex.org/W1717365219","https://openalex.org/W1917913112","https://openalex.org/W1992787746","https://openalex.org/W2000397086","https://openalex.org/W2073021822","https://openalex.org/W2091734240","https://openalex.org/W2123859926","https://openalex.org/W2158534713","https://openalex.org/W2165526004","https://openalex.org/W2334483166","https://openalex.org/W2613685575","https://openalex.org/W2886300330","https://openalex.org/W2902045097","https://openalex.org/W2964971560","https://openalex.org/W2995652570","https://openalex.org/W3011301837","https://openalex.org/W3011938749","https://openalex.org/W3014461592","https://openalex.org/W3103608420","https://openalex.org/W3119522489","https://openalex.org/W3120361527","https://openalex.org/W3124125511","https://openalex.org/W3133518278","https://openalex.org/W4213224499","https://openalex.org/W4288079730"],"related_works":["https://openalex.org/W2058674645","https://openalex.org/W1594539819","https://openalex.org/W2007257620","https://openalex.org/W2766845742","https://openalex.org/W4213038553","https://openalex.org/W2130867670","https://openalex.org/W1984029386","https://openalex.org/W4312202637","https://openalex.org/W2136513242","https://openalex.org/W2336040088"],"abstract_inverted_index":{"In":[0,49],"computer-aided":[1],"drug":[2],"design,":[3],"the":[4,27,54,58,92,120,127,133],"rapid":[5],"identification":[6],"of":[7,57,84,122],"drugs":[8],"is":[9,20,126],"critical":[10],"for":[11,63,71,132],"combating":[12],"diseases.":[13],"A":[14],"key":[15],"method":[16],"in":[17,97],"this":[18,50,125],"field":[19],"molecular":[21,78,129],"docking,":[22],"which":[23],"aims":[24],"to":[25,109,114],"predict":[26],"interactions":[28],"between":[29],"two":[30],"molecules.":[31],"Molecular":[32],"docking":[33,79,130],"involves":[34],"long":[35],"simulations":[36],"running":[37],"compute-intensive":[38],"algorithms,":[39],"and":[40,73,107,116],"thus,":[41],"can":[42],"profit":[43],"a":[44,76,82,110],"lot":[45],"from":[46],"hardware-based":[47],"acceleration.":[48],"work,":[51],"we":[52,67,88],"investigate":[53],"performance":[55],"efficiency":[56],"SX-Aurora":[59,93,134],"TSUBASA":[60,94],"vector":[61],"computer":[62],"such":[64],"simulations.":[65],"Specifically,":[66],"present":[68],"our":[69,123],"methodology":[70],"porting":[72],"optimizing":[74],"AutoDock,":[75],"widely-used":[77],"program.":[80],"Using":[81],"number":[83],"platform-specific":[85],"code":[86],"optimizations,":[87],"achieved":[89],"executions":[90],"on":[91,102],"that":[95],"are":[96],"average":[98],"3.6\u00d7":[99],"faster":[100],"than":[101],"modern":[103],"128-core":[104],"CPU":[105],"servers,":[106],"up":[108],"certain":[111],"extent,":[112],"competitive":[113],"V100":[115],"A100":[117],"GPUs.":[118],"To":[119],"best":[121],"knowledge,":[124],"first":[128],"implementation":[131],"TSUBASA.":[135]},"counts_by_year":[{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2021-09-27T00:00:00"}
