{"id":"https://openalex.org/W3212324398","doi":"https://doi.org/10.1145/3503470.3503471","title":"ParaFold: Paralleling AlphaFold for Large-Scale Predictions","display_name":"ParaFold: Paralleling AlphaFold for Large-Scale Predictions","publication_year":2022,"publication_date":"2022-01-11","ids":{"openalex":"https://openalex.org/W3212324398","doi":"https://doi.org/10.1145/3503470.3503471","mag":"3212324398"},"language":"en","primary_location":{"id":"doi:10.1145/3503470.3503471","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3503470.3503471","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Conference on High Performance Computing in Asia-Pacific Region Workshops","raw_type":"proceedings-article"},"type":"preprint","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/A5090728932","display_name":"Bozitao Zhong","orcid":"https://orcid.org/0000-0001-9363-6099"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bozitao Zhong","raw_affiliation_strings":["Center for High Performance Computing, Shanghai Jiao Tong University, China"],"affiliations":[{"raw_affiliation_string":"Center for High Performance Computing, Shanghai Jiao Tong University, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103113595","display_name":"Xiaoming Su","orcid":"https://orcid.org/0009-0006-9425-1098"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoming Su","raw_affiliation_strings":["Center for High Performance Computing, Shanghai Jiao Tong University, China"],"affiliations":[{"raw_affiliation_string":"Center for High Performance Computing, Shanghai Jiao Tong University, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062120797","display_name":"Minhua Wen","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Minhua Wen","raw_affiliation_strings":["Center for High Performance Computing, Shanghai Jiao Tong University, China"],"affiliations":[{"raw_affiliation_string":"Center for High Performance Computing, Shanghai Jiao Tong University, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059451062","display_name":"Si-Cheng Zuo","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sicheng Zuo","raw_affiliation_strings":["Center for High Performance Computing, Shanghai Jiao Tong University, China"],"affiliations":[{"raw_affiliation_string":"Center for High Performance Computing, Shanghai Jiao Tong University, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047704765","display_name":"Liang Hong","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liang Hong","raw_affiliation_strings":["Institute of Natural Sciences, Shanghai Jiao Tong University, China"],"affiliations":[{"raw_affiliation_string":"Institute of Natural Sciences, Shanghai Jiao Tong University, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062471441","display_name":"James Lin","orcid":"https://orcid.org/0000-0003-4404-5027"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"James Lin","raw_affiliation_strings":["Center for High Performance Computing, Shanghai Jiao Tong University, China"],"affiliations":[{"raw_affiliation_string":"Center for High Performance Computing, Shanghai Jiao Tong University, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5090728932"],"corresponding_institution_ids":["https://openalex.org/I183067930"],"apc_list":null,"apc_paid":null,"fwci":2.513,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.900743,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9984999895095825,"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":0.9984999895095825,"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":0.9950000047683716,"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"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9923999905586243,"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":0.7848148345947266},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6996769905090332},{"id":"https://openalex.org/keywords/compiler","display_name":"Compiler","score":0.5885676741600037},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5643981695175171},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.506332278251648},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.4709304869174957},{"id":"https://openalex.org/keywords/gpu-cluster","display_name":"GPU cluster","score":0.45564138889312744},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.38942477107048035},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.32322800159454346},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09516391158103943}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7848148345947266},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6996769905090332},{"id":"https://openalex.org/C169590947","wikidata":"https://www.wikidata.org/wiki/Q47506","display_name":"Compiler","level":2,"score":0.5885676741600037},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5643981695175171},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.506332278251648},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.4709304869174957},{"id":"https://openalex.org/C2781335571","wikidata":"https://www.wikidata.org/wiki/Q2633544","display_name":"GPU cluster","level":3,"score":0.45564138889312744},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.38942477107048035},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.32322800159454346},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09516391158103943},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3503470.3503471","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3503470.3503471","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Conference on High Performance Computing in Asia-Pacific Region Workshops","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W2026699081","https://openalex.org/W2052345596","https://openalex.org/W2096344315","https://openalex.org/W2102461176","https://openalex.org/W2138122982","https://openalex.org/W2142961247","https://openalex.org/W2557595285","https://openalex.org/W2735621019","https://openalex.org/W2774178591","https://openalex.org/W2949342052","https://openalex.org/W2950954328","https://openalex.org/W2953008890","https://openalex.org/W2968494487","https://openalex.org/W2984894304","https://openalex.org/W3104537585","https://openalex.org/W3136918052","https://openalex.org/W3177828909","https://openalex.org/W3178087467","https://openalex.org/W3183475563","https://openalex.org/W3194955130","https://openalex.org/W3202105508","https://openalex.org/W3204490060","https://openalex.org/W3205544459","https://openalex.org/W3207457994","https://openalex.org/W3208622370"],"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":{"AlphaFold":[0,34,50,73,126,262],"developed":[1],"by":[2,26,198,289],"DeepMind":[3],"predicts":[4],"protein":[5,20,32,87,130,189,249,314],"structures":[6],"from":[7,43],"the":[8,18,39,70,90,111,135,154,164,193,216,223,248,270,286,313],"amino":[9],"acid":[10],"sequence":[11],"at":[12,297],"or":[13],"near":[14],"experimental":[15],"resolution,":[16],"solving":[17],"50-year-old":[19],"folding":[21],"challenge,":[22],"leading":[23],"to":[24,45,79,89,140,146,229],"progress":[25],"transforming":[27],"large-scale":[28,114,142,194],"genomics":[29],"data":[30],"into":[31],"structures.":[33],"will":[35,305],"also":[36,151],"greatly":[37,306],"change":[38],"scientific":[40],"research":[41],"model":[42,65,200],"low-throughput":[44],"high-throughput":[46,282,309],"manner.":[47],"The":[48,301],"overall":[49],"prediction":[51,167,196,251],"process":[52],"consists":[53],"of":[54,84,113,125,166,187,203,253,269,303],"two":[55,160],"stages:":[56],"1)":[57],"MSA":[58,82],"construction":[59,83],"based":[60],"on":[61,67,172,179,211,291],"CPUs":[62,75,173],"and":[63,94,109,137,145,156,174,219,278,296,311],"2)":[64],"inferences":[66],"GPUs.":[68,180],"In":[69],"first":[71],"stage,":[72],"uses":[74],"only,":[76],"taking":[77],"up":[78,308],"hours":[80,210,235],"for":[81,127,281],"a":[85,240,258,298],"single":[86],"due":[88],"large":[91],"database":[92],"sizes":[93],"I/O":[95],"bottlenecks.":[96],"However,":[97],"GPUs":[98],"in":[99,105,208],"this":[100,264],"stage":[101],"remain":[102],"idle,":[103],"resulting":[104],"low":[106],"GPU":[107,138,148,157,225,242,254],"utilization":[108],"restricting":[110],"capacity":[112,252],"structure":[115,131,143,195,250,283],"predictions.":[116,132],"Therefore,":[117],"we":[118],"proposed":[119],"\u201cParaFold\u201d,":[120],"an":[121,276],"open-source":[122],"parallel":[123],"version":[124],"high":[128],"throughput":[129],"ParaFold":[133,150,183,245,274,304],"separates":[134],"CPU":[136,155],"parts":[139],"enable":[141],"predictions":[144],"improve":[147],"utilization.":[149],"effectively":[152],"reduces":[153],"runtime":[158,226,243],"with":[159,184,233,263,293],"optimizations":[161],"without":[162],"compromising":[163],"quality":[165],"results:":[168],"using":[169,175,237],"multi-threaded":[170],"parallelism":[171],"optimized":[176],"JAX":[177,220],"compilation":[178],"We":[181,191],"evaluated":[182],"three":[185],"datasets":[186],"different":[188],"lengths.":[190],"showed":[192],"capability":[197],"running":[199,290],"1":[201],"inference":[202],"\u223c":[204],"20,000":[205,267],"small":[206],"proteins":[207,268],"5.4":[209,230],"one":[212],"NVIDIA":[213],"DGX-2.":[214],"With":[215],"CPU/GPU":[217],"separation":[218],"compile":[221],"optimization,":[222],"total":[224],"was":[227],"reduced":[228],"hours,":[231],"compared":[232],"1,352.6":[234],"when":[236],"AlphaFold,":[238],"achieving":[239],"99.7%":[241],"reduction.":[244],"largely":[246],"increased":[247],"per":[255],"day,":[256],"getting":[257],"250X":[259],"speedup":[260],"over":[261],"case":[265],"(\u223c":[266],"same":[271],"50":[272],"residues).":[273],"offers":[275],"rapid":[277],"effective":[279],"approach":[280],"predictions,":[284],"leveraging":[285],"predictive":[287],"power":[288],"supercomputers,":[292],"shorter":[294],"time":[295],"lower":[299],"cost.":[300],"development":[302],"speed":[307],"studies":[310],"render":[312],"\u201cstructure-omics\u201d":[315],"feasible.":[316]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-31T07:56:22.981413","created_date":"2025-10-10T00:00:00"}