{"id":"https://openalex.org/W2081056566","doi":"https://doi.org/10.1145/2506583.2506693","title":"MEGADOCK-GPU","display_name":"MEGADOCK-GPU","publication_year":2013,"publication_date":"2013-09-22","ids":{"openalex":"https://openalex.org/W2081056566","doi":"https://doi.org/10.1145/2506583.2506693","mag":"2081056566"},"language":"en","primary_location":{"id":"doi:10.1145/2506583.2506693","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2506583.2506693","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/2506583.2506693","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/2506583.2506693","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064806463","display_name":"Takehiro Shimoda","orcid":null},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takehiro Shimoda","raw_affiliation_strings":["Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN and Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN and Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004756730","display_name":"Takashi Ishida","orcid":"https://orcid.org/0000-0002-9478-3223"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takashi Ishida","raw_affiliation_strings":["Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN","Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN","institution_ids":["https://openalex.org/I114531698"]},{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN#TAB#","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111451849","display_name":"Shuji Suzuki","orcid":null},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]},{"id":"https://openalex.org/I205924995","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I1319490839","https://openalex.org/I205924995"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Shuji Suzuki","raw_affiliation_strings":["Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN and Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN and Research Fellow of the Japan Society for the Promotion of Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN and Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN and Research Fellow of the Japan Society for the Promotion of Science","institution_ids":["https://openalex.org/I114531698","https://openalex.org/I205924995"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061510293","display_name":"Masahito Ohue","orcid":"https://orcid.org/0000-0002-0120-1643"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]},{"id":"https://openalex.org/I205924995","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I1319490839","https://openalex.org/I205924995"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masahito Ohue","raw_affiliation_strings":["Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN and Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN and Research Fellow of the Japan Society for the Promotion of Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN and Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN and Research Fellow of the Japan Society for the Promotion of Science","institution_ids":["https://openalex.org/I114531698","https://openalex.org/I205924995"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067025136","display_name":"Yutaka Akiyama","orcid":"https://orcid.org/0000-0003-2863-8703"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yutaka Akiyama","raw_affiliation_strings":["Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN and Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN and Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, JAPAN","institution_ids":["https://openalex.org/I114531698"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"883","last_page":"889"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9973000288009644,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9919999837875366,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7921394109725952},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.6923619508743286},{"id":"https://openalex.org/keywords/interactome","display_name":"Interactome","score":0.6628145575523376},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.6258932948112488},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5654065608978271},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.5513442158699036},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.541718065738678},{"id":"https://openalex.org/keywords/gpu-cluster","display_name":"GPU cluster","score":0.4473056197166443},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.41849732398986816},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.17843827605247498},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.12079790234565735},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.11341136693954468}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7921394109725952},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6923619508743286},{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.6628145575523376},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.6258932948112488},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5654065608978271},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.5513442158699036},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.541718065738678},{"id":"https://openalex.org/C2781335571","wikidata":"https://www.wikidata.org/wiki/Q2633544","display_name":"GPU cluster","level":3,"score":0.4473056197166443},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.41849732398986816},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.17843827605247498},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.12079790234565735},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.11341136693954468},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2506583.2506693","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2506583.2506693","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/2506583.2506693","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/2506583.2506693","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2506583.2506693","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/2506583.2506693","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2081056566.pdf","grobid_xml":"https://content.openalex.org/works/W2081056566.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W76842085","https://openalex.org/W1472797403","https://openalex.org/W1529184047","https://openalex.org/W1965379872","https://openalex.org/W1988739180","https://openalex.org/W2000383223","https://openalex.org/W2021343666","https://openalex.org/W2055905702","https://openalex.org/W2058071327","https://openalex.org/W2062414926","https://openalex.org/W2065279209","https://openalex.org/W2094547935","https://openalex.org/W2102182691","https://openalex.org/W2102312699","https://openalex.org/W2118795098","https://openalex.org/W2128796532","https://openalex.org/W2142485291","https://openalex.org/W2148356001","https://openalex.org/W2150056503","https://openalex.org/W2155417823","https://openalex.org/W2157991822","https://openalex.org/W2171249995","https://openalex.org/W2915344963"],"related_works":["https://openalex.org/W2056717482","https://openalex.org/W3189307731","https://openalex.org/W2949962288","https://openalex.org/W2364686214","https://openalex.org/W1428699136","https://openalex.org/W1998560227","https://openalex.org/W2017587301","https://openalex.org/W2030707850","https://openalex.org/W2170611190","https://openalex.org/W2566934642"],"abstract_inverted_index":{"Protein-protein":[0],"docking":[1,40,50,77,130,137],"is":[2,47,55,62,147],"a":[3,37,90,100,114],"method":[4,41],"for":[5,57],"predicting":[6],"the":[7,23,134],"protein":[8,13,16,67,142],"complex":[9],"structure":[10],"from":[11],"monomeric":[12],"structures.":[14],"Because":[15],"structural":[17],"information":[18],"has":[19,26,42],"been":[20,27,43],"increased":[21],"and":[22,97,110],"application":[24,135],"field":[25],"expanded":[28],"to":[29,139],"more":[30,53],"difficult":[31],"ones":[32],"such":[33],"as":[34],"interactome":[35,59],"prediction,":[36,60],"faster":[38,121],"protein-protein":[39,49,76],"eagerly":[44],"demanded.":[45],"MEGADOCK":[46,123],"fast":[48],"software":[51,78,131],"but":[52],"acceleration":[54],"demanded":[56],"an":[58,74],"which":[61],"composed":[63],"of":[64,66,136],"millions":[65],"pairs.":[68],"In":[69],"this":[70],"paper,":[71],"we":[72],"developed":[73],"ultra-fast":[75],"named":[79],"MEGADOCK-GPU":[80,105,146],"by":[81],"using":[82],"general":[83],"purpose":[84],"GPU":[85],"computing":[86],"techniques.":[87],"We":[88],"implemented":[89],"system":[91],"that":[92,117],"utilizes":[93],"all":[94],"CPU":[95,108,126],"cores":[96,109],"GPUs":[98,112],"in":[99],"computation":[101],"node.":[102],"As":[103],"results,":[104],"on":[106,124],"12":[107],"3":[111],"achieved":[113],"calculation":[115],"speed":[116],"was":[118],"37.0":[119],"times":[120],"than":[122],"1":[125],"core.":[127],"The":[128],"novel":[129],"will":[132],"facilitate":[133],"techniques":[138],"assist":[140],"large-scale":[141],"interaction":[143],"network":[144],"analyses.":[145],"freely":[148],"available":[149],"at":[150],"http://www.bi.cs.titech.ac.jp/megadock/gpu/.":[151]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2016-06-24T00:00:00"}
