{"id":"https://openalex.org/W2944472564","doi":"https://doi.org/10.1145/3310273.3323426","title":"An hybrid approach to accelerate a molecular docking application for virtual screening in heterogeneous nodes","display_name":"An hybrid approach to accelerate a molecular docking application for virtual screening in heterogeneous nodes","publication_year":2019,"publication_date":"2019-04-30","ids":{"openalex":"https://openalex.org/W2944472564","doi":"https://doi.org/10.1145/3310273.3323426","mag":"2944472564"},"language":"en","primary_location":{"id":"doi:10.1145/3310273.3323426","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3310273.3323426","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 16th ACM International Conference on Computing Frontiers","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/11311/1160671","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045006433","display_name":"Emanuele Vitali","orcid":"https://orcid.org/0000-0001-8629-2099"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"E. Vitali","raw_affiliation_strings":["Politecnico di Milano, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059293847","display_name":"Davide Gadioli","orcid":"https://orcid.org/0000-0002-0143-0737"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"D. Gadioli","raw_affiliation_strings":["Politecnico di Milano, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032283822","display_name":"Andrea R. Beccari","orcid":"https://orcid.org/0000-0001-6830-2695"},"institutions":[{"id":"https://openalex.org/I4210140932","display_name":"Domp\u00e9 (Italy)","ror":"https://ror.org/04erezm33","country_code":"IT","type":"company","lineage":["https://openalex.org/I4210140932"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"A. Beccari","raw_affiliation_strings":["Domp\u00e9 Farmaceutici SpA, L'Aquila, Via Campo di Pile, Italy"],"affiliations":[{"raw_affiliation_string":"Domp\u00e9 Farmaceutici SpA, L'Aquila, Via Campo di Pile, Italy","institution_ids":["https://openalex.org/I4210140932"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029838099","display_name":"Carlo Cavazzoni","orcid":"https://orcid.org/0000-0002-9589-4785"},"institutions":[{"id":"https://openalex.org/I4210119786","display_name":"Cineca","ror":"https://ror.org/02f013h18","country_code":"IT","type":"other","lineage":["https://openalex.org/I4210119786"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"C. Cavazzoni","raw_affiliation_strings":["Cineca, Bologna, Italy"],"affiliations":[{"raw_affiliation_string":"Cineca, Bologna, Italy","institution_ids":["https://openalex.org/I4210119786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031461662","display_name":"Cristina Silvano","orcid":"https://orcid.org/0000-0003-1668-0883"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"C. Silvano","raw_affiliation_strings":["Politecnico di Milano, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077005193","display_name":"Gianluca Palermo","orcid":"https://orcid.org/0000-0001-7955-8012"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"G. Palermo","raw_affiliation_strings":["Politecnico di Milano, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5045006433"],"corresponding_institution_ids":["https://openalex.org/I93860229"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07042254,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"298","last_page":"299"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9984999895095825,"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":0.9984999895095825,"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":0.989799976348877,"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/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9889000058174133,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8022115230560303},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.7006962299346924},{"id":"https://openalex.org/keywords/porting","display_name":"Porting","score":0.6984467506408691},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5940451622009277},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.3680662512779236},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3358207941055298},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.20446956157684326},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1536223292350769},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.12886828184127808}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8022115230560303},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.7006962299346924},{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.6984467506408691},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5940451622009277},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3680662512779236},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3358207941055298},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.20446956157684326},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1536223292350769},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.12886828184127808},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"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/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3310273.3323426","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3310273.3323426","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 16th ACM International Conference on Computing Frontiers","raw_type":"proceedings-article"},{"id":"pmh:oai:re.public.polimi.it:11311/1160671","is_oa":true,"landing_page_url":"http://hdl.handle.net/11311/1160671","pdf_url":null,"source":{"id":"https://openalex.org/S4306400312","display_name":"Virtual Community of Pathological Anatomy (University of Castilla La Mancha)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79189158","host_organization_name":"University of Castilla-La Mancha","host_organization_lineage":["https://openalex.org/I79189158"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"pmh:oai:re.public.polimi.it:11311/1160671","is_oa":true,"landing_page_url":"http://hdl.handle.net/11311/1160671","pdf_url":null,"source":{"id":"https://openalex.org/S4306400312","display_name":"Virtual Community of Pathological Anatomy (University of Castilla La Mancha)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79189158","host_organization_name":"University of Castilla-La Mancha","host_organization_lineage":["https://openalex.org/I79189158"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferenceObject"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4609934410","display_name":null,"funder_award_id":"671623","funder_id":"https://openalex.org/F4320338336","funder_display_name":"H2020 Future and Emerging Technologies"}],"funders":[{"id":"https://openalex.org/F4320338336","display_name":"H2020 Future and Emerging Technologies","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":4,"referenced_works":["https://openalex.org/W2094385413","https://openalex.org/W2578119541","https://openalex.org/W2891512882","https://openalex.org/W2903046887"],"related_works":["https://openalex.org/W2059230675","https://openalex.org/W2376003823","https://openalex.org/W2773493604","https://openalex.org/W2269591907","https://openalex.org/W2027065525","https://openalex.org/W2057846043","https://openalex.org/W2093426296","https://openalex.org/W2336040088","https://openalex.org/W4402273478","https://openalex.org/W2594726310"],"abstract_inverted_index":{"Molecular":[0,84],"Docking":[1,85],"is":[2,29,54],"a":[3,22,42,46,83,116,131],"crucial":[4],"task":[5,13,53],"in":[6,15,31],"the":[7,16,19,25,32,36,73,98,108,120,125,136],"process":[8,39],"of":[9,18,21,35,45,49,66,72,119],"Drug":[10],"Discovery.":[11],"This":[12,52],"consists":[14],"estimation":[17],"position":[20],"molecule":[23,50],"inside":[24],"docking":[26,74],"site.":[27],"It":[28],"used":[30],"early":[33],"stages":[34],"drug":[37],"discovery":[38],"to":[40,63,70,87,114,124],"perform":[41],"virtual":[43],"screening":[44],"large":[47],"library":[48],"candidates.":[51],"usually":[55],"performed":[56],"using":[57],"High":[58],"Performance":[59],"Computing":[60],"platforms,":[61],"due":[62,69],"sheer":[64],"number":[65],"candidates":[67],"and":[68,81,102],"complexity":[71],"problem.":[75],"In":[76],"this":[77],"work":[78],"we":[79,111],"ported":[80],"optimized":[82],"Module":[86],"an":[88],"heterogeneous":[89],"system":[90],"with":[91,107],"one":[92],"or":[93],"more":[94],"GPGPU":[95],"accelerators,":[96],"leveraging":[97],"directive":[99],"languages":[100],"OpenMP":[101],"OpenACC.":[103],"We":[104],"show":[105],"that":[106],"proposed":[109],"approach,":[110],"are":[112],"able":[113],"reach":[115],"better":[117],"utilization":[118],"available":[121],"resources":[122],"compared":[123],"usual":[126],"CPU/GPU":[127],"data":[128],"splitting,":[129],"reaching":[130],"25%":[132],"throughput":[133],"improvement":[134],"within":[135],"single":[137],"node.":[138]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2019-05-16T00:00:00"}
