{"id":"https://openalex.org/W3125566655","doi":"https://doi.org/10.1021/acs.jcim.0c01060","title":"Accelerating <i>De Novo</i> Drug Design against Novel Proteins Using Deep Learning","display_name":"Accelerating <i>De Novo</i> Drug Design against Novel Proteins Using Deep Learning","publication_year":2021,"publication_date":"2021-01-25","ids":{"openalex":"https://openalex.org/W3125566655","doi":"https://doi.org/10.1021/acs.jcim.0c01060","mag":"3125566655","pmid":"https://pubmed.ncbi.nlm.nih.gov/33491455"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c01060","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c01060","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/A5102810785","display_name":"Sowmya Ramaswamy Krishnan","orcid":"https://orcid.org/0000-0001-5404-3266"},"institutions":[{"id":"https://openalex.org/I55215948","display_name":"Tata Consultancy Services (India)","ror":"https://ror.org/01b9n8m42","country_code":"IN","type":"company","lineage":["https://openalex.org/I4210086519","https://openalex.org/I55215948"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sowmya Ramaswamy Krishnan","raw_affiliation_strings":["TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad 500081, India"],"raw_orcid":"https://orcid.org/0000-0001-5404-3266","affiliations":[{"raw_affiliation_string":"TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad 500081, India","institution_ids":["https://openalex.org/I55215948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027584199","display_name":"Navneet Bung","orcid":"https://orcid.org/0000-0002-6376-277X"},"institutions":[{"id":"https://openalex.org/I55215948","display_name":"Tata Consultancy Services (India)","ror":"https://ror.org/01b9n8m42","country_code":"IN","type":"company","lineage":["https://openalex.org/I4210086519","https://openalex.org/I55215948"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Navneet Bung","raw_affiliation_strings":["TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad 500081, India"],"raw_orcid":"https://orcid.org/0000-0002-6376-277X","affiliations":[{"raw_affiliation_string":"TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad 500081, India","institution_ids":["https://openalex.org/I55215948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018990576","display_name":"Gopalakrishnan Bulusu","orcid":"https://orcid.org/0000-0002-4958-7573"},"institutions":[{"id":"https://openalex.org/I55215948","display_name":"Tata Consultancy Services (India)","ror":"https://ror.org/01b9n8m42","country_code":"IN","type":"company","lineage":["https://openalex.org/I4210086519","https://openalex.org/I55215948"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Gopalakrishnan Bulusu","raw_affiliation_strings":["TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad 500081, India"],"raw_orcid":"https://orcid.org/0000-0002-4958-7573","affiliations":[{"raw_affiliation_string":"TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad 500081, India","institution_ids":["https://openalex.org/I55215948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042990614","display_name":"Arijit Roy","orcid":"https://orcid.org/0000-0002-1961-2483"},"institutions":[{"id":"https://openalex.org/I55215948","display_name":"Tata Consultancy Services (India)","ror":"https://ror.org/01b9n8m42","country_code":"IN","type":"company","lineage":["https://openalex.org/I4210086519","https://openalex.org/I55215948"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Arijit Roy","raw_affiliation_strings":["TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad 500081, India"],"raw_orcid":"https://orcid.org/0000-0002-1961-2483","affiliations":[{"raw_affiliation_string":"TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad 500081, India","institution_ids":["https://openalex.org/I55215948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5018990576","https://openalex.org/A5042990614"],"corresponding_institution_ids":["https://openalex.org/I55215948"],"apc_list":null,"apc_paid":null,"fwci":9.6264,"has_fulltext":false,"cited_by_count":91,"citation_normalized_percentile":{"value":0.98454176,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"61","issue":"2","first_page":"621","last_page":"630"},"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9732999801635742,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9545000195503235,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6759010553359985},{"id":"https://openalex.org/keywords/drug-target","display_name":"Drug target","score":0.622708261013031},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5718536972999573},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5652441382408142},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5572999715805054},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5511231422424316},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5294729471206665},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.4957514703273773},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4122258126735687},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3691054582595825},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.18161603808403015},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10421055555343628},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.08721548318862915}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6759010553359985},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.622708261013031},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5718536972999573},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5652441382408142},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5572999715805054},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5511231422424316},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5294729471206665},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4957514703273773},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4122258126735687},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3691054582595825},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.18161603808403015},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10421055555343628},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.08721548318862915},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","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},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.0c01060","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c01060","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:33491455","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33491455","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":[{"score":0.550000011920929,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":71,"referenced_works":["https://openalex.org/W1483308173","https://openalex.org/W1505823450","https://openalex.org/W1516230275","https://openalex.org/W1518367201","https://openalex.org/W1612638707","https://openalex.org/W1924770834","https://openalex.org/W1976499671","https://openalex.org/W1981387370","https://openalex.org/W1984994707","https://openalex.org/W1997772366","https://openalex.org/W2008589980","https://openalex.org/W2013416851","https://openalex.org/W2020646428","https://openalex.org/W2036153681","https://openalex.org/W2038702914","https://openalex.org/W2043509228","https://openalex.org/W2044172327","https://openalex.org/W2046133002","https://openalex.org/W2055043387","https://openalex.org/W2056171219","https://openalex.org/W2057477511","https://openalex.org/W2060531713","https://openalex.org/W2063657897","https://openalex.org/W2067092722","https://openalex.org/W2109154308","https://openalex.org/W2110025562","https://openalex.org/W2113364934","https://openalex.org/W2120524849","https://openalex.org/W2128124948","https://openalex.org/W2134017175","https://openalex.org/W2134967712","https://openalex.org/W2159659449","https://openalex.org/W2160592148","https://openalex.org/W2165168652","https://openalex.org/W2166637863","https://openalex.org/W2171268876","https://openalex.org/W2187089797","https://openalex.org/W2279387906","https://openalex.org/W2313170240","https://openalex.org/W2517981151","https://openalex.org/W2540499968","https://openalex.org/W2564034046","https://openalex.org/W2578240541","https://openalex.org/W2605908560","https://openalex.org/W2610148085","https://openalex.org/W2773987374","https://openalex.org/W2805489776","https://openalex.org/W2886980930","https://openalex.org/W2887280559","https://openalex.org/W2889555425","https://openalex.org/W2895763047","https://openalex.org/W2901411193","https://openalex.org/W2902858390","https://openalex.org/W2923585142","https://openalex.org/W2945500496","https://openalex.org/W2949626814","https://openalex.org/W2949986955","https://openalex.org/W2952524552","https://openalex.org/W2953128081","https://openalex.org/W2954094311","https://openalex.org/W2963028280","https://openalex.org/W2964067969","https://openalex.org/W2964121744","https://openalex.org/W2989100760","https://openalex.org/W3000348967","https://openalex.org/W3019676419","https://openalex.org/W3027975282","https://openalex.org/W3081574977","https://openalex.org/W3100751385","https://openalex.org/W3136918052","https://openalex.org/W4214717370"],"related_works":["https://openalex.org/W4308805210","https://openalex.org/W2553548503","https://openalex.org/W3045995536","https://openalex.org/W1967404732","https://openalex.org/W2226749982","https://openalex.org/W1968386238","https://openalex.org/W4308253407","https://openalex.org/W4353017618","https://openalex.org/W4310831746","https://openalex.org/W3206915023"],"abstract_inverted_index":{"In":[0,26,56],"the":[1,5,16,44,59,95,98,104,108,123,126,137,170,177,188,195,206,209],"world":[2],"plagued":[3],"by":[4,166],"emergence":[6],"of":[7,46,61,89,94,97,107,125,140,176,187,208],"new":[8,22,154],"diseases,":[9],"it":[10],"is":[11,84],"essential":[12],"that":[13],"we":[14],"accelerate":[15],"drug":[17,38,73],"design":[18,74,153,199],"process":[19],"to":[20,70,111,121,135,152,190],"develop":[21,71],"therapeutics":[23],"against":[24,52,169],"them.":[25],"recent":[27],"years,":[28],"deep":[29,62,130],"learning-based":[30],"methods":[31,42],"have":[32],"shown":[33],"some":[34],"success":[35],"in":[36],"ligand-based":[37],"design.":[39],"Yet,":[40],"these":[41,145],"face":[43],"problem":[45],"data":[47],"scarcity":[48],"while":[49],"designing":[50,167],"drugs":[51],"a":[53,72],"novel":[54],"target.":[55],"this":[57],"work,":[58],"potential":[60,207],"learning":[63,118,151],"and":[64,198],"molecular":[65],"modeling":[66],"approaches":[67],"was":[68,119,133,164],"leveraged":[69],"pipeline,":[75],"which":[76],"can":[77],"be":[78],"useful":[79],"for":[80,183],"cases":[81],"where":[82,174],"there":[83],"limited":[85],"or":[86],"no":[87],"availability":[88],"target-specific":[90,115,127],"ligand":[91],"datasets.":[92],"Inhibitors":[93],"homologues":[96],"target":[99,109],"protein":[100,110],"were":[101,147,181],"screened":[102],"at":[103],"active":[105],"site":[106],"create":[112],"an":[113,158],"initial":[114],"dataset.":[116,128],"Transfer":[117],"used":[120,182],"learn":[122],"features":[124],"A":[129],"predictive":[131],"model":[132],"utilized":[134],"predict":[136],"docking":[138,160],"scores":[139],"newly":[141],"designed":[142],"molecules.":[143],"Both":[144],"models":[146],"combined":[148],"using":[149],"reinforcement":[150],"chemical":[155],"entities":[156],"with":[157,201],"optimized":[159],"score.":[161],"The":[162,185],"pipeline":[163],"validated":[165],"inhibitors":[168,180],"human":[171],"JAK2":[172,179],"protein,":[173],"none":[175],"existing":[178,192],"training.":[184],"ability":[186],"method":[189],"reproduce":[191],"molecules":[193,200],"from":[194],"validation":[196],"dataset":[197],"better":[202],"binding":[203],"energy":[204],"demonstrates":[205],"proposed":[210],"approach.":[211]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":22},{"year":2022,"cited_by_count":20},{"year":2021,"cited_by_count":20},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-16T13:24:37.021932","created_date":"2025-10-10T00:00:00"}