{"id":"https://openalex.org/W3023570844","doi":"https://doi.org/10.1007/s11227-020-03295-x","title":"Tunable approximations to control time-to-solution in an HPC molecular docking Mini-App","display_name":"Tunable approximations to control time-to-solution in an HPC molecular docking Mini-App","publication_year":2021,"publication_date":"2021-01-01","ids":{"openalex":"https://openalex.org/W3023570844","doi":"https://doi.org/10.1007/s11227-020-03295-x","mag":"3023570844"},"language":"en","primary_location":{"id":"pmh:oai:re.public.polimi.it:11311/1160670","is_oa":true,"landing_page_url":"http://hdl.handle.net/11311/1160670","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/article"},"type":"article","indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/11311/1160670","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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":true,"raw_author_name":"Gadioli D.","raw_affiliation_strings":["Dipartimento di Elettronica, Infomazione e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Infomazione e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","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":"Palermo G.","raw_affiliation_strings":["Dipartimento di Elettronica, Infomazione e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Infomazione e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068012553","display_name":"Stefano Cherubin","orcid":"https://orcid.org/0000-0002-5579-5942"},"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":"Cherubin S.","raw_affiliation_strings":["Dipartimento di Elettronica, Infomazione e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Infomazione e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","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":false,"raw_author_name":"Vitali E.","raw_affiliation_strings":["Dipartimento di Elettronica, Infomazione e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Infomazione e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069191452","display_name":"Giovanni Agosta","orcid":"https://orcid.org/0000-0002-0255-4475"},"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":"Agosta G.","raw_affiliation_strings":["Dipartimento di Elettronica, Infomazione e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Infomazione e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067593514","display_name":"Candida Manelfi","orcid":"https://orcid.org/0000-0002-9175-243X"},"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":"Manelfi C.","raw_affiliation_strings":["Dompe' Farmaceutici SpA Research Center, L'Aquila, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dompe' Farmaceutici SpA Research Center, L'Aquila, Italy","institution_ids":["https://openalex.org/I4210140932"]}]},{"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":"Beccari A. R.","raw_affiliation_strings":["Dompe' Farmaceutici SpA Research Center, L'Aquila, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dompe' Farmaceutici SpA Research Center, L'Aquila, 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":"Cavazzoni C.","raw_affiliation_strings":["Supercomputing Innovation and Application Department, CINECA, Bologna, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Supercomputing Innovation and Application Department, CINECA, Bologna, Italy","institution_ids":["https://openalex.org/I4210119786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033005482","display_name":"Nico Sanna","orcid":"https://orcid.org/0000-0002-1947-7939"},"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":"Sanna N.","raw_affiliation_strings":["Supercomputing Innovation and Application Department, CINECA, Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Supercomputing Innovation and Application Department, CINECA, Rome, Italy","institution_ids":["https://openalex.org/I4210119786"]}]},{"author_position":"last","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":"Silvano C.","raw_affiliation_strings":["Dipartimento di Elettronica, Infomazione e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Infomazione e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5059293847"],"corresponding_institution_ids":["https://openalex.org/I93860229"],"apc_list":null,"apc_paid":null,"fwci":1.0656,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.79709638,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9986000061035156,"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":0.9986000061035156,"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":0.9915000200271606,"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":0.9821000099182129,"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/virtual-screening","display_name":"Virtual screening","score":0.8530322313308716},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8407737016677856},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.6063418388366699},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5479757785797119},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5417168736457825},{"id":"https://openalex.org/keywords/chemical-space","display_name":"Chemical space","score":0.4784529209136963},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.461546927690506},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.41300565004348755},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3461902141571045},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22359636425971985},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10669609904289246}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.8530322313308716},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8407737016677856},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6063418388366699},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5479757785797119},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5417168736457825},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.4784529209136963},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.461546927690506},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.41300565004348755},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3461902141571045},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22359636425971985},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10669609904289246},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:re.public.polimi.it:11311/1160670","is_oa":true,"landing_page_url":"http://hdl.handle.net/11311/1160670","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/article"}],"best_oa_location":{"id":"pmh:oai:re.public.polimi.it:11311/1160670","is_oa":true,"landing_page_url":"http://hdl.handle.net/11311/1160670","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/article"},"sustainable_development_goals":[{"score":0.4099999964237213,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G4496196766","display_name":null,"funder_award_id":"ANTAREX - 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":64,"referenced_works":["https://openalex.org/W1513150088","https://openalex.org/W1517566065","https://openalex.org/W1592950931","https://openalex.org/W1974977468","https://openalex.org/W1978880553","https://openalex.org/W1984576237","https://openalex.org/W1985588649","https://openalex.org/W1986240377","https://openalex.org/W1998305460","https://openalex.org/W2002042437","https://openalex.org/W2020217519","https://openalex.org/W2026005150","https://openalex.org/W2030922317","https://openalex.org/W2031390939","https://openalex.org/W2033088400","https://openalex.org/W2038763636","https://openalex.org/W2039724126","https://openalex.org/W2043855224","https://openalex.org/W2044833910","https://openalex.org/W2047509756","https://openalex.org/W2050456292","https://openalex.org/W2052492157","https://openalex.org/W2052643996","https://openalex.org/W2052919707","https://openalex.org/W2067913710","https://openalex.org/W2076823955","https://openalex.org/W2094190665","https://openalex.org/W2094385413","https://openalex.org/W2099625934","https://openalex.org/W2102182691","https://openalex.org/W2103300124","https://openalex.org/W2110118331","https://openalex.org/W2111444234","https://openalex.org/W2115318272","https://openalex.org/W2119299853","https://openalex.org/W2121546953","https://openalex.org/W2130479394","https://openalex.org/W2135653967","https://openalex.org/W2137321308","https://openalex.org/W2142883190","https://openalex.org/W2147370410","https://openalex.org/W2148556017","https://openalex.org/W2163491234","https://openalex.org/W2170881177","https://openalex.org/W2178590834","https://openalex.org/W2244005500","https://openalex.org/W2265166184","https://openalex.org/W2318331847","https://openalex.org/W2319130110","https://openalex.org/W2417987166","https://openalex.org/W2463731436","https://openalex.org/W2544480501","https://openalex.org/W2580767461","https://openalex.org/W2624885502","https://openalex.org/W2751150280","https://openalex.org/W2770677425","https://openalex.org/W2798846955","https://openalex.org/W2898099374","https://openalex.org/W2903046887","https://openalex.org/W2921262115","https://openalex.org/W2964252755","https://openalex.org/W4234496834","https://openalex.org/W4235600583","https://openalex.org/W4251875201"],"related_works":["https://openalex.org/W3174709249","https://openalex.org/W2017055503","https://openalex.org/W3185720802","https://openalex.org/W4387472361","https://openalex.org/W2059230675","https://openalex.org/W2376003823","https://openalex.org/W2773493604","https://openalex.org/W2269591907","https://openalex.org/W2921092150","https://openalex.org/W2027065525"],"abstract_inverted_index":{"The":[0,224],"drug":[1,75],"discovery":[2,76],"process":[3],"involves":[4],"several":[5],"tasks":[6],"to":[7,59,69,112,128,148,184,242,252],"be":[8,67,88],"performed":[9,23],"in":[10,12,15,24,115,245],"vivo,":[11],"vitro":[13],"and":[14,139,150,172,222],"silico.":[16,25],"Molecular":[17],"docking":[18,86,130,198],"is":[19,48],"a":[20,34,54,116,164,185,191,210,216,228],"task":[21,47,162],"typically":[22],"It":[26],"aims":[27],"at":[28],"finding":[29],"the":[30,41,61,70,74,79,83,92,96,102,106,109,125,141,152,159,177,201,206,253,256],"three-dimensional":[31],"pose":[32],"of":[33,57,73,82,95,108,158,166,220,236,255],"given":[35],"molecule":[36],"when":[37],"it":[38],"interacts":[39],"with":[40,144,238],"target":[42],"protein":[43],"binding":[44],"site.":[45],"This":[46],"often":[49],"done":[50],"for":[51],"virtual":[52,160,257],"screening":[53,161,258],"huge":[55,80],"set":[56],"molecules":[58],"find":[60],"most":[62],"promising":[63],"ones,":[64],"which":[65],"will":[66],"forwarded":[68],"later":[71],"stages":[72],"process.":[77],"Given":[78],"complexity":[81],"problem,":[84],"molecular":[85,129,197],"cannot":[87],"solved":[89],"by":[90,104,131,194,214],"exploring":[91],"entire":[93],"space":[94,107],"ligand":[97,110],"poses.":[98],"State-of-the-art":[99],"approaches":[100],"face":[101],"problem":[103],"sampling":[105],"poses":[111],"generate":[113],"results":[114],"reasonable":[117],"time":[118,187],"budget.":[119,188],"In":[120,135],"this":[121],"work,":[122],"we":[123,137],"improve":[124],"geometric":[126],"approach":[127,226],"introducing":[132],"tunable":[133,145],"approximations.":[134],"particular,":[136],"analysed":[138],"enriched":[140],"original":[142],"implementation":[143],"software":[146,167],"knobs":[147],"explore":[149],"control":[151],"performance-accuracy":[153],"trade-offs.":[154],"We":[155,189,204],"modelled":[156],"time-to-solution":[157,229],"as":[163],"function":[165],"knobs,":[168],"input":[169],"data":[170],"features,":[171],"available":[173],"computational":[174],"resources.":[175],"Therefore,":[176],"application":[178],"can":[179],"autotune":[180],"its":[181],"configuration":[182],"according":[183,251],"user-defined":[186],"used":[190],"Mini-App":[192,208],"derived":[193],"LiGenDock\u2014a":[195],"state-of-the-art":[196],"application\u2014to":[199],"validate":[200],"proposed":[202,225],"approach.":[203],"run":[205],"enhanced":[207],"on":[209],"high-performance":[211],"computing":[212],"system":[213],"using":[215],"very":[217],"large":[218],"database":[219],"pockets":[221],"ligands.":[223],"exposes":[227],"interval":[230],"spanning":[231],"more":[232,244],"than":[233],"one":[234],"order":[235],"magnitude":[237],"accuracy":[239,249],"degradation":[240],"up":[241],"30%,":[243],"general":[246],"providing":[247],"different":[248],"levels":[250],"needs":[254],"campaign.":[259]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-05-03T08:25:01.440150","created_date":"2020-05-13T00:00:00"}
