{"id":"https://openalex.org/W4289821392","doi":"https://doi.org/10.1109/tpds.2022.3194916","title":"Redesigning and Optimizing UCSF DOCK3.7 on Sunway TaihuLight","display_name":"Redesigning and Optimizing UCSF DOCK3.7 on Sunway TaihuLight","publication_year":2022,"publication_date":"2022-08-05","ids":{"openalex":"https://openalex.org/W4289821392","doi":"https://doi.org/10.1109/tpds.2022.3194916"},"language":"en","primary_location":{"id":"doi:10.1109/tpds.2022.3194916","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tpds.2022.3194916","pdf_url":null,"source":{"id":"https://openalex.org/S97130795","display_name":"IEEE Transactions on Parallel and Distributed Systems","issn_l":"1045-9219","issn":["1045-9219","1558-2183","2161-9883"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Parallel and Distributed Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038527513","display_name":"Kai Xu","orcid":"https://orcid.org/0000-0002-0907-2671"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210158984","display_name":"National Supercomputing Center in Wuxi","ror":"https://ror.org/04ypjrs34","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210158984"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kai Xu","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China","National Supercomputing Center in Wuxi, Wuxi, China"],"raw_orcid":"https://orcid.org/0000-0002-0907-2671","affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"National Supercomputing Center in Wuxi, Wuxi, China","institution_ids":["https://openalex.org/I4210158984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107093628","display_name":"Jinxiao Zhang","orcid":"https://orcid.org/0009-0002-3203-0426"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210158984","display_name":"National Supercomputing Center in Wuxi","ror":"https://ror.org/04ypjrs34","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210158984"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinxiao Zhang","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China","National Supercomputing Center in Wuxi, Wuxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"National Supercomputing Center in Wuxi, Wuxi, China","institution_ids":["https://openalex.org/I4210158984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003075115","display_name":"Xiaohui Duan","orcid":"https://orcid.org/0000-0002-1913-6683"},"institutions":[{"id":"https://openalex.org/I4210158984","display_name":"National Supercomputing Center in Wuxi","ror":"https://ror.org/04ypjrs34","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210158984"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaohui Duan","raw_affiliation_strings":["Department of Computer Science and Technology, Tsinghua University, Beijing, China","National Supercomputing Center in Wuxi, Wuxi, China"],"raw_orcid":"https://orcid.org/0000-0002-1913-6683","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"National Supercomputing Center in Wuxi, Wuxi, China","institution_ids":["https://openalex.org/I4210158984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038022821","display_name":"Xiaobo Wan","orcid":"https://orcid.org/0000-0003-4288-9074"},"institutions":[{"id":"https://openalex.org/I4210139958","display_name":"Beijing Computational Science Research Center","ror":"https://ror.org/04tavf782","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210139958"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaobo Wan","raw_affiliation_strings":["Computational Medicine (Beijing) Co. Ltd, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Medicine (Beijing) Co. Ltd, Beijing, China","institution_ids":["https://openalex.org/I4210139958"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074665620","display_name":"Niu Huang","orcid":"https://orcid.org/0000-0002-6912-033X"},"institutions":[{"id":"https://openalex.org/I4210086405","display_name":"National Institute of Biological Sciences, Beijing","ror":"https://ror.org/00wksha49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210086405"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Niu Huang","raw_affiliation_strings":["National Institute of Biological Sciences, Beijing, China","Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Biological Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210086405"]},{"raw_affiliation_string":"Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bertil Schmidt","raw_affiliation_strings":["Institute for Computer Science, Johannes Gutenberg University, Mainz, Germany"],"raw_orcid":"https://orcid.org/0000-0003-2597-8331","affiliations":[{"raw_affiliation_string":"Institute for Computer Science, Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100620772","display_name":"Weiguo Liu","orcid":"https://orcid.org/0000-0001-8834-0453"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210158984","display_name":"National Supercomputing Center in Wuxi","ror":"https://ror.org/04ypjrs34","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210158984"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiguo Liu","raw_affiliation_strings":["School of Software, Shandong University, Jinan, China","National Supercomputing Center in Wuxi, Wuxi, China"],"raw_orcid":"https://orcid.org/0000-0001-8834-0453","affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"National Supercomputing Center in Wuxi, Wuxi, China","institution_ids":["https://openalex.org/I4210158984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101678397","display_name":"Guangwen Yang","orcid":"https://orcid.org/0000-0002-8673-8254"},"institutions":[{"id":"https://openalex.org/I4210158984","display_name":"National Supercomputing Center in Wuxi","ror":"https://ror.org/04ypjrs34","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210158984"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guangwen Yang","raw_affiliation_strings":["Department of Computer Science and Technology, Tsinghua University, Beijing, China","National Supercomputing Center in Wuxi, Wuxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"National Supercomputing Center in Wuxi, Wuxi, China","institution_ids":["https://openalex.org/I4210158984"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.7606,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.74396029,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":97},"biblio":{"volume":"33","issue":"12","first_page":"4458","last_page":"4471"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9839000105857849,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":0.9781000018119812,"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":0.8226426243782043},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.6990261077880859},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5958366394042969},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.5851569175720215},{"id":"https://openalex.org/keywords/mmx","display_name":"MMX","score":0.5240095853805542},{"id":"https://openalex.org/keywords/asynchronous-communication","display_name":"Asynchronous communication","score":0.4972396194934845},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.45446696877479553},{"id":"https://openalex.org/keywords/directory","display_name":"Directory","score":0.4415318965911865},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3560020327568054},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2963131368160248},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.16703307628631592}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8226426243782043},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.6990261077880859},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5958366394042969},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.5851569175720215},{"id":"https://openalex.org/C85918911","wikidata":"https://www.wikidata.org/wiki/Q904336","display_name":"MMX","level":2,"score":0.5240095853805542},{"id":"https://openalex.org/C151319957","wikidata":"https://www.wikidata.org/wiki/Q752739","display_name":"Asynchronous communication","level":2,"score":0.4972396194934845},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.45446696877479553},{"id":"https://openalex.org/C2777683733","wikidata":"https://www.wikidata.org/wiki/Q201456","display_name":"Directory","level":2,"score":0.4415318965911865},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3560020327568054},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2963131368160248},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.16703307628631592},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tpds.2022.3194916","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tpds.2022.3194916","pdf_url":null,"source":{"id":"https://openalex.org/S97130795","display_name":"IEEE Transactions on Parallel and Distributed Systems","issn_l":"1045-9219","issn":["1045-9219","1558-2183","2161-9883"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Parallel and Distributed Systems","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4140447210","display_name":"\u9762\u5411\u8d85\u5927\u89c4\u6a21\u77ed\u8bfb\u751f\u7269\u5e8f\u5217\u6570\u636e\u7684\u9ad8\u6027\u80fd\u5339\u914d\u7b97\u6cd5\u7814\u7a76","funder_award_id":"61972231","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4521563595","display_name":null,"funder_award_id":"U1806205","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1543525056","https://openalex.org/W1757990252","https://openalex.org/W1834677900","https://openalex.org/W1917913112","https://openalex.org/W1980285986","https://openalex.org/W1985588649","https://openalex.org/W2000350990","https://openalex.org/W2005925339","https://openalex.org/W2044444984","https://openalex.org/W2050456292","https://openalex.org/W2067643341","https://openalex.org/W2103300124","https://openalex.org/W2105668062","https://openalex.org/W2108389384","https://openalex.org/W2121621209","https://openalex.org/W2132617221","https://openalex.org/W2134967712","https://openalex.org/W2164255317","https://openalex.org/W2329758767","https://openalex.org/W2728256789","https://openalex.org/W2732801577","https://openalex.org/W2753374271","https://openalex.org/W2758843674","https://openalex.org/W2761669656","https://openalex.org/W2805045192","https://openalex.org/W2885814935","https://openalex.org/W2888204870","https://openalex.org/W2899133614","https://openalex.org/W2906734242","https://openalex.org/W2908799171","https://openalex.org/W2912012512","https://openalex.org/W2912171584","https://openalex.org/W2963613550","https://openalex.org/W3010016408","https://openalex.org/W3040885852","https://openalex.org/W3047757922","https://openalex.org/W3091854778","https://openalex.org/W3094640617","https://openalex.org/W3120361527","https://openalex.org/W4288079730","https://openalex.org/W6639979234","https://openalex.org/W6757501586","https://openalex.org/W6757974227","https://openalex.org/W6764490040"],"related_works":["https://openalex.org/W1534961658","https://openalex.org/W35209463","https://openalex.org/W2544823983","https://openalex.org/W1595089495","https://openalex.org/W2168758875","https://openalex.org/W2410733619","https://openalex.org/W4246549241","https://openalex.org/W2963483475","https://openalex.org/W1876383975","https://openalex.org/W2943610686"],"abstract_inverted_index":{"Molecular":[0],"docking":[1,66],"is":[2,25,37,58],"the":[3,13,31,61,78,84,116,150,154,161,222,238,276],"process":[4],"of":[5,16,54,60,86,156,205,213,221,231,245,255,270,272],"posing,":[6],"scoring,":[7],"and":[8,73,98,123,177,211],"ranking":[9],"small":[10],"molecules":[11],"at":[12],"binding":[14],"sites":[15],"proteins":[17],"to":[18,47,102,114,129,160,168,181,192,217,242,268],"prioritize":[19],"compounds":[20],"for":[21,120],"experimental":[22],"testing.":[23],"It":[24],"a":[26,38,43,91,109,157,203,229,243,258],"widely-used":[27],"computational":[28],"method":[29],"in":[30,52,100,184,190],"drug":[32],"discovery":[33],"process.":[34],"However,":[35],"it":[36],"highly":[39],"time-consuming":[40],"procedure":[41],"since":[42],"receptor":[44],"may":[45],"need":[46],"find":[48],"favorable":[49],"ligand":[50,121,131,158,194],"orientations":[51,195],"billions":[53],"ligands.":[55],"UCSF":[56,75],"DOCK3.7":[57,76],"one":[59],"most":[62],"widely":[63],"used":[64],"molecular":[65],"applications.":[67],"In":[68,199],"this":[69],"paper,":[70],"we":[71,89,107,163,174,201],"port":[72],"optimize":[74],"on":[77,257,275],"Sunway":[79,278],"TaihuLight":[80],"supercomputer.":[81,279],"To":[82],"avoid":[83],"impact":[85],"load":[87],"imbalance,":[88],"employ":[90],"producer-consumer":[92],"strategy":[93],"that":[94,135,228],"can":[95,139,233],"overlap":[96],"I/O":[97,141],"computation":[99,214],"order":[101,191],"achieve":[103],"high":[104,197],"performance.":[105],"Furthermore,":[106,173,262],"present":[108,164],"new":[110],"binary":[111],"file":[112,118,137],"format":[113,119,138],"replace":[115],"mol2db2":[117],"storage":[122],"adopt":[124],"xzip":[125,145],"rather":[126],"than":[127],"gzip":[128],"compress":[130,178],"files.":[132],"We":[133],"show":[134,227],"our":[136,251,263],"reduce":[140],"time":[142],"significantly":[143],"while":[144],"saves":[146],"significant":[147],"storage.":[148],"For":[149],"routines":[151],"which":[152],"determine":[153],"orientation":[155],"relative":[159],"receptor,":[162],"an":[165,246],"improved":[166],"algorithm":[167],"discard":[169],"geometrically":[170],"similar":[171],"orientations.":[172],"fuse":[175],"loops":[176],"memory":[179],"usage":[180],"store":[182],"data":[183,209],"fast":[185],"Local":[186],"Device":[187],"Memory":[188],"(LDM)":[189],"score":[193],"with":[196],"efficiency.":[198],"addition,":[200],"propose":[202],"number":[204],"architecture-specific":[206],"optimizations.":[207],"Asynchronous":[208],"transfer":[210],"vectorization":[212],"are":[215],"implemented":[216],"take":[218],"full":[219],"advantage":[220],"SW26010":[223,259],"processor.":[224],"Our":[225],"experiments":[226],"speedup":[230],"167":[232],"be":[234],"achieved":[235],"by":[236],"using":[237],"proposed":[239],"strategies.":[240],"Compared":[241],"core":[244,260],"Intel(R)":[247],"Core(TM)":[248],"i9-10900K":[249],"CPU,":[250],"approach":[252],"achieves":[253,265],"speedups":[254],"15":[256],"group.":[261],"implementation":[264],"strong":[266],"scalability":[267],"hundreds":[269],"thousands":[271],"heterogeneous":[273],"cores":[274],"next-generation":[277]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}