{"id":"https://openalex.org/W4284975662","doi":"https://doi.org/10.1145/3491418.3535181","title":"AlphaFold2 Workflow Optimization for High Throughput Predictions in HPC Environment","display_name":"AlphaFold2 Workflow Optimization for High Throughput Predictions in HPC Environment","publication_year":2022,"publication_date":"2022-07-08","ids":{"openalex":"https://openalex.org/W4284975662","doi":"https://doi.org/10.1145/3491418.3535181"},"language":"en","primary_location":{"id":"doi:10.1145/3491418.3535181","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3491418.3535181","pdf_url":null,"source":{"id":"https://openalex.org/S4306523034","display_name":"Practice and Experience in Advanced Research Computing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing","raw_type":"proceedings-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/A5035238240","display_name":"E. Posada","orcid":"https://orcid.org/0000-0002-2565-0267"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Edwin Fernando Posada","raw_affiliation_strings":["Temple University, USA"],"affiliations":[{"raw_affiliation_string":"Temple University, USA","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034775141","display_name":"Francisco McGee","orcid":null},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Francisco McGee","raw_affiliation_strings":["Temple University, USA"],"affiliations":[{"raw_affiliation_string":"Temple University, USA","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000977599","display_name":"Richard Berger","orcid":"https://orcid.org/0000-0002-3044-8266"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard Berger","raw_affiliation_strings":["Temple University, USA"],"affiliations":[{"raw_affiliation_string":"Temple University, USA","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036492755","display_name":"Mitchell Dorrell","orcid":"https://orcid.org/0000-0003-1002-7410"},"institutions":[{"id":"https://openalex.org/I35765314","display_name":"Pittsburgh Supercomputing Center","ror":"https://ror.org/04tac1482","country_code":"US","type":"facility","lineage":["https://openalex.org/I35765314"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mitchell Dorrell","raw_affiliation_strings":["Pittsburgh Supercomputing Center, USA"],"affiliations":[{"raw_affiliation_string":"Pittsburgh Supercomputing Center, USA","institution_ids":["https://openalex.org/I35765314"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076384273","display_name":"Jason J. Lamanna","orcid":"https://orcid.org/0000-0002-1357-6901"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason Lamanna","raw_affiliation_strings":["Temple University, USA"],"affiliations":[{"raw_affiliation_string":"Temple University, USA","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030401879","display_name":"S. Sanielevici","orcid":"https://orcid.org/0000-0002-3171-8563"},"institutions":[{"id":"https://openalex.org/I35765314","display_name":"Pittsburgh Supercomputing Center","ror":"https://ror.org/04tac1482","country_code":"US","type":"facility","lineage":["https://openalex.org/I35765314"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergiu Sanielevici","raw_affiliation_strings":["Pittsburgh Supercomputing Center, USA"],"affiliations":[{"raw_affiliation_string":"Pittsburgh Supercomputing Center, USA","institution_ids":["https://openalex.org/I35765314"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049873048","display_name":"Vincenzo Carnevale","orcid":"https://orcid.org/0000-0002-0447-1278"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vincenzo Carnevale","raw_affiliation_strings":["Temple University, USA"],"affiliations":[{"raw_affiliation_string":"Temple University, USA","institution_ids":["https://openalex.org/I84392919"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5035238240"],"corresponding_institution_ids":["https://openalex.org/I84392919"],"apc_list":null,"apc_paid":null,"fwci":0.4238,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.80632635,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9801999926567078,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.7943360805511475},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7526625394821167},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7274137735366821},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.4426094591617584},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3951132297515869},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3266356587409973},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2879928648471832},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.19519227743148804}],"concepts":[{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.7943360805511475},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7526625394821167},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7274137735366821},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.4426094591617584},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3951132297515869},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3266356587409973},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2879928648471832},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.19519227743148804},{"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:10.1145/3491418.3535181","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3491418.3535181","pdf_url":null,"source":{"id":"https://openalex.org/S4306523034","display_name":"Practice and Experience in Advanced Research Computing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5199999809265137,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2029667189","https://openalex.org/W2102461176","https://openalex.org/W2904361469","https://openalex.org/W2913820882","https://openalex.org/W2984894304","https://openalex.org/W3112830812","https://openalex.org/W3177828909","https://openalex.org/W3185307588","https://openalex.org/W3198923619","https://openalex.org/W3212324398","https://openalex.org/W4221148791"],"related_works":["https://openalex.org/W2384867379","https://openalex.org/W4400094300","https://openalex.org/W2329539859","https://openalex.org/W2227905990","https://openalex.org/W2765823764","https://openalex.org/W3214280620","https://openalex.org/W3191490922","https://openalex.org/W2794038527","https://openalex.org/W2327638088","https://openalex.org/W1599154403"],"abstract_inverted_index":{"In":[0,17],"this":[1,18],"work,":[2],"we":[3,20],"propose":[4],"a":[5,13],"high-throughput":[6],"implementation":[7],"that":[8],"executes":[9],"AlphaFold2":[10],"efficiently":[11],"in":[12,41],"High-Performance":[14],"Computing":[15],"environment.":[16],"case,":[19],"have":[21],"tested":[22],"our":[23],"proposed":[24],"workflow":[25],"with":[26],"the":[27,45,49,66],"T1050":[28],"CASP14":[29],"sequence":[30],"on":[31],"PSC\u2019s":[32],"Bridges-2":[33],"HPC":[34],"system.":[35],"The":[36],"results":[37],"showed":[38],"an":[39],"improvement":[40],"computation-only":[42],"runtimes":[43],"and":[44],"opportunity":[46],"to":[47,60],"reuse":[48],"protein":[50],"databases":[51],"when":[52],"calculating":[53],"many":[54],"structures":[55],"simultaneously,":[56],"which":[57],"would":[58],"lead":[59],"massive":[61],"time":[62],"savings":[63],"while":[64],"maximizing":[65],"utilization":[67],"of":[68],"computing":[69],"resources.":[70]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}