{"id":"https://openalex.org/W4400879287","doi":"https://doi.org/10.1021/acs.jcim.4c00481","title":"HydraScreen: A Generalizable Structure-Based Deep Learning Approach to Drug Discovery","display_name":"HydraScreen: A Generalizable Structure-Based Deep Learning Approach to Drug Discovery","publication_year":2024,"publication_date":"2024-07-22","ids":{"openalex":"https://openalex.org/W4400879287","doi":"https://doi.org/10.1021/acs.jcim.4c00481","pmid":"https://pubmed.ncbi.nlm.nih.gov/39037942"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c00481","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00481","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/A5055123789","display_name":"Alvaro Prat","orcid":"https://orcid.org/0000-0003-0094-6659"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Alvaro Prat","raw_affiliation_strings":["AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States"],"raw_orcid":"https://orcid.org/0000-0003-0094-6659","affiliations":[{"raw_affiliation_string":"AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031627472","display_name":"Hisham Abdel Aty","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hisham Abdel Aty","raw_affiliation_strings":["AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054350377","display_name":"Orestis Bastas","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Orestis Bastas","raw_affiliation_strings":["AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000823676","display_name":"Gintautas Kamuntavi\u010dius","orcid":"https://orcid.org/0000-0001-5141-4535"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gintautas Kamuntavi\u010dius","raw_affiliation_strings":["AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043001553","display_name":"Tanya Paquet","orcid":"https://orcid.org/0000-0001-8847-3977"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tanya Paquet","raw_affiliation_strings":["AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025230471","display_name":"Povilas Norvai\u0161as","orcid":"https://orcid.org/0000-0003-4790-9820"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Povilas Norvai\u0161as","raw_affiliation_strings":["AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009772769","display_name":"Piero Gasparotto","orcid":"https://orcid.org/0000-0001-7671-4825"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Piero Gasparotto","raw_affiliation_strings":["AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071326210","display_name":"Roy Tal","orcid":"https://orcid.org/0000-0001-8551-2547"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Roy Tal","raw_affiliation_strings":["AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI Chemistry, Ro5 2801 Gateway Drive, Irving, 75063 Texas, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5055123789"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":5.3238,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.96237735,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"64","issue":"15","first_page":"5817","last_page":"5831"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9797999858856201,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.977400004863739,"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/drug-discovery","display_name":"Drug discovery","score":0.7488151788711548},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5220372676849365},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4794429838657379},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4517360329627991},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4470135271549225},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.43685898184776306},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3888927102088928},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.21818110346794128},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.17765864729881287},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.17145097255706787},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09958016872406006}],"concepts":[{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.7488151788711548},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5220372676849365},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4794429838657379},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4517360329627991},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4470135271549225},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.43685898184776306},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3888927102088928},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.21818110346794128},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.17765864729881287},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.17145097255706787},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09958016872406006}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.4c00481","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00481","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:39037942","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39037942","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":87,"referenced_works":["https://openalex.org/W1500036797","https://openalex.org/W1535169733","https://openalex.org/W1653739410","https://openalex.org/W1981076832","https://openalex.org/W1993046136","https://openalex.org/W2009423060","https://openalex.org/W2025816743","https://openalex.org/W2028629022","https://openalex.org/W2029413789","https://openalex.org/W2046850956","https://openalex.org/W2050456292","https://openalex.org/W2073021822","https://openalex.org/W2088970363","https://openalex.org/W2090149270","https://openalex.org/W2092285329","https://openalex.org/W2095719702","https://openalex.org/W2105668062","https://openalex.org/W2114162221","https://openalex.org/W2116423958","https://openalex.org/W2118571345","https://openalex.org/W2129590593","https://openalex.org/W2134967712","https://openalex.org/W2166550586","https://openalex.org/W2169678694","https://openalex.org/W2183050958","https://openalex.org/W2325928434","https://openalex.org/W2335804930","https://openalex.org/W2337496963","https://openalex.org/W2507599630","https://openalex.org/W2587598315","https://openalex.org/W2608559058","https://openalex.org/W2609462956","https://openalex.org/W2741292700","https://openalex.org/W2754993961","https://openalex.org/W2781821160","https://openalex.org/W2784213390","https://openalex.org/W2795523124","https://openalex.org/W2803094965","https://openalex.org/W2808042204","https://openalex.org/W2889677957","https://openalex.org/W2894469531","https://openalex.org/W2913034365","https://openalex.org/W2918239264","https://openalex.org/W2937885053","https://openalex.org/W2947497907","https://openalex.org/W2948831670","https://openalex.org/W2963833291","https://openalex.org/W2969325194","https://openalex.org/W2971801381","https://openalex.org/W2974531988","https://openalex.org/W3005043246","https://openalex.org/W3006477052","https://openalex.org/W3008726875","https://openalex.org/W3009499476","https://openalex.org/W3020511336","https://openalex.org/W3023042104","https://openalex.org/W3027583552","https://openalex.org/W3034675470","https://openalex.org/W3081528324","https://openalex.org/W3082411326","https://openalex.org/W3098189759","https://openalex.org/W3098846260","https://openalex.org/W3103064283","https://openalex.org/W3104508774","https://openalex.org/W3104585744","https://openalex.org/W3120951562","https://openalex.org/W3124411756","https://openalex.org/W3126083771","https://openalex.org/W3135935512","https://openalex.org/W3137154687","https://openalex.org/W3140330522","https://openalex.org/W3167575787","https://openalex.org/W3168430821","https://openalex.org/W3168436232","https://openalex.org/W3185227028","https://openalex.org/W3194618792","https://openalex.org/W3209909976","https://openalex.org/W3217568487","https://openalex.org/W4200139236","https://openalex.org/W4221095602","https://openalex.org/W4283013935","https://openalex.org/W4290805632","https://openalex.org/W4307994819","https://openalex.org/W4308616064","https://openalex.org/W4310222678","https://openalex.org/W4361282512","https://openalex.org/W4386960656"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W2611989081","https://openalex.org/W2480711475","https://openalex.org/W4230611425","https://openalex.org/W2731899572","https://openalex.org/W4294635752","https://openalex.org/W4304166257","https://openalex.org/W4206379684","https://openalex.org/W4383066092","https://openalex.org/W4380075502"],"abstract_inverted_index":{"We":[0,34,51,83,134],"propose":[1],"HydraScreen,":[2],"a":[3,15,85,131,160,164],"deep-learning":[4],"framework":[5],"for":[6,22,39,88,141],"safe":[7],"and":[8,29,42,70,100,128,163],"robust":[9],"accelerated":[10],"drug":[11,49],"discovery.":[12],"HydraScreen":[13,154],"utilizes":[14],"state-of-the-art":[16],"3D":[17],"convolutional":[18],"neural":[19],"network":[20],"designed":[21,35],"the":[23,61,98,112,147,168],"effective":[24],"representation":[25],"of":[26,114,149,171],"molecular":[27],"structures":[28],"interactions":[30],"in":[31,47,68],"protein\u2013ligand":[32,172],"binding.":[33],"an":[36],"end-to-end":[37],"pipeline":[38],"high-throughput":[40],"screening":[41],"lead":[43],"optimization,":[44],"targeting":[45],"applications":[46],"structure-based":[48],"design.":[50],"assessed":[52],"our":[53,115],"approach":[54,87,104],"using":[55],"established":[56],"public":[57,165],"benchmarks":[58],"based":[59],"on":[60],"CASF-2016":[62],"core":[63],"set,":[64],"achieving":[65],"top-tier":[66],"results":[67],"affinity":[69],"pose":[71],"prediction":[72],"(Pearson\u2019s":[73],"r":[74],"=":[75,78,81],"0.86,":[76],"RMSE":[77],"1.15,":[79],"Top-1":[80],"0.95).":[82],"introduced":[84],"novel":[86,126],"interaction":[89],"profiling,":[90],"aimed":[91,144],"at":[92,145,156],"detecting":[93],"potential":[94,139],"biases":[95],"within":[96],"both":[97],"model":[99],"data":[101],"sets.":[102],"This":[103],"not":[105],"only":[106],"enhanced":[107],"interpretability":[108],"but":[109],"also":[110,135],"reinforced":[111],"impartiality":[113],"methodology.":[116],"Finally,":[117],"we":[118],"demonstrated":[119],"HydraScreen\u2019s":[120],"ability":[121],"to":[122],"generalize":[123],"effectively":[124],"across":[125],"proteins":[127],"ligands":[129],"through":[130],"temporal":[132],"split.":[133],"provide":[136],"insights":[137],"into":[138],"avenues":[140],"future":[142],"development":[143],"enhancing":[146],"robustness":[148],"machine":[150],"learning":[151],"scoring":[152],"functions.":[153],"(accessible":[155],"http://hydrascreen.ro5.ai/paper":[157],")":[158],"provides":[159],"user-friendly":[161],"GUI":[162],"API,":[166],"facilitating":[167],"easy-access":[169],"assessment":[170],"complexes.":[173]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-25T08:15:23.626066","created_date":"2025-10-10T00:00:00"}