{"id":"https://openalex.org/W4290075791","doi":"https://doi.org/10.1021/acs.jcim.2c00554","title":"Self-Focusing Virtual Screening with Active Design Space Pruning","display_name":"Self-Focusing Virtual Screening with Active Design Space Pruning","publication_year":2022,"publication_date":"2022-08-06","ids":{"openalex":"https://openalex.org/W4290075791","doi":"https://doi.org/10.1021/acs.jcim.2c00554","pmid":"https://pubmed.ncbi.nlm.nih.gov/35938299"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c00554","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00554","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5017287886","display_name":"David Graff","orcid":"https://orcid.org/0000-0003-1250-3329"},"institutions":[{"id":"https://openalex.org/I4210110987","display_name":"IIT@MIT","ror":"https://ror.org/01wp8zh54","country_code":"US","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210110987"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David E. Graff","raw_affiliation_strings":["Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02142, United States","Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02142, United States","institution_ids":["https://openalex.org/I4210110987"]},{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056535696","display_name":"Matteo Aldeghi","orcid":"https://orcid.org/0000-0003-0019-8806"},"institutions":[{"id":"https://openalex.org/I4210110987","display_name":"IIT@MIT","ror":"https://ror.org/01wp8zh54","country_code":"US","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210110987"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matteo Aldeghi","raw_affiliation_strings":["Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02142, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02142, United States","institution_ids":["https://openalex.org/I4210110987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072958773","display_name":"Joseph A. Morrone","orcid":"https://orcid.org/0000-0001-8550-4854"},"institutions":[{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph A. Morrone","raw_affiliation_strings":["Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10594, United States"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10594, United States","institution_ids":["https://openalex.org/I4210114115"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040280528","display_name":"Kirk E. Jordan","orcid":"https://orcid.org/0000-0001-5148-4437"},"institutions":[{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kirk E. Jordan","raw_affiliation_strings":["IBM Thomas J. Watson Research Center, Cambridge, Massachusetts 02142, United States"],"affiliations":[{"raw_affiliation_string":"IBM Thomas J. Watson Research Center, Cambridge, Massachusetts 02142, United States","institution_ids":["https://openalex.org/I4210114115"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084050064","display_name":"Edward O. Pyzer\u2010Knapp","orcid":"https://orcid.org/0000-0002-8232-8282"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Edward O. Pyzer-Knapp","raw_affiliation_strings":["IBM Research Europe, Daresbury, Warrington WA4 4AD, United Kingdom"],"affiliations":[{"raw_affiliation_string":"IBM Research Europe, Daresbury, Warrington WA4 4AD, United Kingdom","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076162644","display_name":"Connor W. Coley","orcid":"https://orcid.org/0000-0002-8271-8723"},"institutions":[{"id":"https://openalex.org/I4210110987","display_name":"IIT@MIT","ror":"https://ror.org/01wp8zh54","country_code":"US","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210110987"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Connor W. Coley","raw_affiliation_strings":["Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02142, United States","Department of Electrical Engineering and Computer Science, MIT, Cambridge, Massachusetts 02142, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02142, United States","institution_ids":["https://openalex.org/I4210110987"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, MIT, Cambridge, Massachusetts 02142, United States","institution_ids":["https://openalex.org/I4210110987"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5076162644"],"corresponding_institution_ids":["https://openalex.org/I4210110987"],"apc_list":null,"apc_paid":null,"fwci":2.3234,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.8902527,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"62","issue":"16","first_page":"3854","last_page":"3862"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9990000128746033,"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"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9990000128746033,"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/T12535","display_name":"Machine Learning and Data Classification","score":0.9883999824523926,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9876999855041504,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7412227988243103},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6370244026184082},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6100912094116211},{"id":"https://openalex.org/keywords/overhead","display_name":"Overhead (engineering)","score":0.5533678531646729},{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.5484058856964111},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.5435755848884583},{"id":"https://openalex.org/keywords/digital-signal-processing","display_name":"Digital signal processing","score":0.4639553427696228},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3808882534503937},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3764885663986206},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32834184169769287},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.158946692943573},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10735556483268738},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.07983165979385376}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7412227988243103},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6370244026184082},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6100912094116211},{"id":"https://openalex.org/C2779960059","wikidata":"https://www.wikidata.org/wiki/Q7113681","display_name":"Overhead (engineering)","level":2,"score":0.5533678531646729},{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.5484058856964111},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5435755848884583},{"id":"https://openalex.org/C84462506","wikidata":"https://www.wikidata.org/wiki/Q173142","display_name":"Digital signal processing","level":2,"score":0.4639553427696228},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3808882534503937},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3764885663986206},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32834184169769287},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.158946692943573},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10735556483268738},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.07983165979385376},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","level":1,"score":0.0},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","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}],"mesh":[{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.2c00554","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00554","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:35938299","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35938299","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"No poverty","score":0.6100000143051147,"id":"https://metadata.un.org/sdg/1"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1560021816","https://openalex.org/W1675620121","https://openalex.org/W1678620623","https://openalex.org/W1968871273","https://openalex.org/W1984994707","https://openalex.org/W1991238353","https://openalex.org/W2002009218","https://openalex.org/W2061789405","https://openalex.org/W2097968133","https://openalex.org/W2108389384","https://openalex.org/W2112724747","https://openalex.org/W2123241324","https://openalex.org/W2131686485","https://openalex.org/W2166566250","https://openalex.org/W2337110853","https://openalex.org/W2437591545","https://openalex.org/W2587942483","https://openalex.org/W2782634521","https://openalex.org/W2783201493","https://openalex.org/W2789547262","https://openalex.org/W2807081771","https://openalex.org/W2901292178","https://openalex.org/W2912171584","https://openalex.org/W2945551948","https://openalex.org/W2966357564","https://openalex.org/W2978512279","https://openalex.org/W3010016408","https://openalex.org/W3014154196","https://openalex.org/W3025462781","https://openalex.org/W3027975282","https://openalex.org/W3044724994","https://openalex.org/W3112474878","https://openalex.org/W3112559629","https://openalex.org/W3113331478","https://openalex.org/W3135642867","https://openalex.org/W3144567229","https://openalex.org/W3159598019","https://openalex.org/W3208515103","https://openalex.org/W3210246971","https://openalex.org/W3214234430","https://openalex.org/W4200233821","https://openalex.org/W4211218744","https://openalex.org/W4220798957","https://openalex.org/W4240374930"],"related_works":["https://openalex.org/W3180887190","https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W2320211095","https://openalex.org/W2308164565","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2062768126","https://openalex.org/W188202134","https://openalex.org/W2029380707"],"abstract_inverted_index":{"High-throughput":[0],"virtual":[1,29],"screening":[2],"is":[3,21],"an":[4,27,75,134],"indispensable":[5],"technique":[6,89],"utilized":[7],"in":[8,46,121,145],"the":[9,17,24,60,63,78,107,129],"discovery":[10],"of":[11,19,26,80,109,114,137],"small":[12],"molecules.":[13],"In":[14,70],"cases":[15],"where":[16,148],"library":[18],"molecules":[20],"exceedingly":[22],"large,":[23],"cost":[25],"exhaustive":[28],"screen":[30],"may":[31],"be":[32],"prohibitive.":[33],"Model-guided":[34],"optimization":[35,82,115,139,146],"has":[36],"been":[37],"employed":[38],"to":[39,50,59,77,92,111,128,154],"lower":[40],"these":[41,54,149],"costs":[42,58,86,123,144,150],"through":[43,62],"dramatic":[44],"increases":[45],"sample":[47],"efficiency":[48],"compared":[49],"random":[51],"selection.":[52],"However,":[53],"techniques":[55],"introduce":[56],"new":[57],"workflow":[61],"surrogate":[64],"model":[65],"training":[66],"and":[67,117],"inference":[68,85],"steps.":[69],"this":[71],"study,":[72],"we":[73,90],"propose":[74],"extension":[76,136],"framework":[79],"model-guided":[81,138],"that":[83,140],"mitigates":[84],"using":[87],"a":[88,112],"refer":[91],"as":[93,158],"design":[94],"space":[95],"pruning":[96],"(DSP),":[97],"which":[98],"irreversibly":[99],"removes":[100],"poor-performing":[101],"candidates":[102],"from":[103],"consideration.":[104],"We":[105],"study":[106],"application":[108],"DSP":[110,132],"variety":[113],"tasks":[116],"observe":[118],"significant":[119],"reductions":[120],"overhead":[122,143],"while":[124],"exhibiting":[125],"similar":[126],"performance":[127],"baseline":[130],"optimization.":[131],"represents":[133],"attractive":[135],"can":[141],"limit":[142],"settings":[147],"are":[151],"non-negligible":[152],"relative":[153],"objective":[155],"costs,":[156],"such":[157],"docking.":[159]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":13}],"updated_date":"2026-03-14T08:43:22.919905","created_date":"2025-10-10T00:00:00"}
