{"id":"https://openalex.org/W2982872869","doi":"https://doi.org/10.1021/acs.jcim.9b01053","title":"AMPL: A Data-Driven Modeling Pipeline for Drug Discovery","display_name":"AMPL: A Data-Driven Modeling Pipeline for Drug Discovery","publication_year":2020,"publication_date":"2020-04-03","ids":{"openalex":"https://openalex.org/W2982872869","doi":"https://doi.org/10.1021/acs.jcim.9b01053","mag":"2982872869","pmid":"https://pubmed.ncbi.nlm.nih.gov/32243153"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b01053","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01053","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.9b01053","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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":["arxiv","crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.9b01053","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003684324","display_name":"Amanda Minnich","orcid":"https://orcid.org/0000-0001-8191-5322"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amanda J. Minnich","raw_affiliation_strings":["Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States","Lawrence livermore National Laboratory"],"raw_orcid":"https://orcid.org/0000-0001-8191-5322","affiliations":[{"raw_affiliation_string":"Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]},{"raw_affiliation_string":"Lawrence livermore National Laboratory","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013155084","display_name":"Kevin McLoughlin","orcid":"https://orcid.org/0000-0001-9651-4951"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin McLoughlin","raw_affiliation_strings":["Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States","Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore California 94550, United States"],"raw_orcid":"https://orcid.org/0000-0001-9651-4951","affiliations":[{"raw_affiliation_string":"Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]},{"raw_affiliation_string":"Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077479510","display_name":"Margaret J. Tse","orcid":null},"institutions":[{"id":"https://openalex.org/I4210114143","display_name":"GlaxoSmithKline (United States)","ror":"https://ror.org/025vn3989","country_code":"US","type":"company","lineage":["https://openalex.org/I188950975","https://openalex.org/I4210114143"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Margaret Tse","raw_affiliation_strings":["GlaxoSmithKline, 5 Crescent Drive Philadelphia Pennsylvania 19112, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GlaxoSmithKline, 5 Crescent Drive Philadelphia Pennsylvania 19112, United States","institution_ids":["https://openalex.org/I4210114143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020011173","display_name":"Jason Deng","orcid":null},"institutions":[{"id":"https://openalex.org/I4210114143","display_name":"GlaxoSmithKline (United States)","ror":"https://ror.org/025vn3989","country_code":"US","type":"company","lineage":["https://openalex.org/I188950975","https://openalex.org/I4210114143"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason Deng","raw_affiliation_strings":["GlaxoSmithKline, 5 Crescent Drive Philadelphia Pennsylvania 19112, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GlaxoSmithKline, 5 Crescent Drive Philadelphia Pennsylvania 19112, United States","institution_ids":["https://openalex.org/I4210114143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016108114","display_name":"Andrew Weber","orcid":"https://orcid.org/0000-0001-6952-5081"},"institutions":[{"id":"https://openalex.org/I4210114143","display_name":"GlaxoSmithKline (United States)","ror":"https://ror.org/025vn3989","country_code":"US","type":"company","lineage":["https://openalex.org/I188950975","https://openalex.org/I4210114143"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew Weber","raw_affiliation_strings":["GlaxoSmithKline, 5 Crescent Drive Philadelphia Pennsylvania 19112, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GlaxoSmithKline, 5 Crescent Drive Philadelphia Pennsylvania 19112, United States","institution_ids":["https://openalex.org/I4210114143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013928614","display_name":"Neha Murad","orcid":"https://orcid.org/0000-0002-8470-3613"},"institutions":[{"id":"https://openalex.org/I4210114143","display_name":"GlaxoSmithKline (United States)","ror":"https://ror.org/025vn3989","country_code":"US","type":"company","lineage":["https://openalex.org/I188950975","https://openalex.org/I4210114143"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Neha Murad","raw_affiliation_strings":["GlaxoSmithKline, 5 Crescent Drive Philadelphia Pennsylvania 19112, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GlaxoSmithKline, 5 Crescent Drive Philadelphia Pennsylvania 19112, United States","institution_ids":["https://openalex.org/I4210114143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084597625","display_name":"Benjamin D. Madej","orcid":null},"institutions":[{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin D. Madej","raw_affiliation_strings":["Frederick National Laboratory, 8560 Progress Drive, Frederick, Maryland 21701, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Frederick National Laboratory, 8560 Progress Drive, Frederick, Maryland 21701, United States","institution_ids":["https://openalex.org/I4210130649"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039641760","display_name":"Bharath Ramsundar","orcid":"https://orcid.org/0000-0001-8450-4262"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bharath Ramsundar","raw_affiliation_strings":["Computable, San Francisco, California 94111, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computable, San Francisco, California 94111, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060494420","display_name":"Tom Rush","orcid":null},"institutions":[{"id":"https://openalex.org/I4210114143","display_name":"GlaxoSmithKline (United States)","ror":"https://ror.org/025vn3989","country_code":"US","type":"company","lineage":["https://openalex.org/I188950975","https://openalex.org/I4210114143"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tom Rush","raw_affiliation_strings":["GlaxoSmithKline, 5 Crescent Drive Philadelphia Pennsylvania 19112, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GlaxoSmithKline, 5 Crescent Drive Philadelphia Pennsylvania 19112, United States","institution_ids":["https://openalex.org/I4210114143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031825885","display_name":"Stacie Calad-Thomson","orcid":null},"institutions":[{"id":"https://openalex.org/I4210114143","display_name":"GlaxoSmithKline (United States)","ror":"https://ror.org/025vn3989","country_code":"US","type":"company","lineage":["https://openalex.org/I188950975","https://openalex.org/I4210114143"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stacie Calad-Thomson","raw_affiliation_strings":["GlaxoSmithKline, 5 Crescent Drive Philadelphia Pennsylvania 19112, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GlaxoSmithKline, 5 Crescent Drive Philadelphia Pennsylvania 19112, United States","institution_ids":["https://openalex.org/I4210114143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012840613","display_name":"Jim Brase","orcid":null},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jim Brase","raw_affiliation_strings":["Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States","Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore California 94550, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]},{"raw_affiliation_string":"Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035849909","display_name":"Jonathan Allen","orcid":"https://orcid.org/0000-0002-4359-8263"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jonathan E. Allen","raw_affiliation_strings":["Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States","Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore California 94550, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]},{"raw_affiliation_string":"Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5035849909"],"corresponding_institution_ids":["https://openalex.org/I1282311441"],"apc_list":null,"apc_paid":null,"fwci":0.3804,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.64810608,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"60","issue":"4","first_page":"1955","last_page":"1968"},"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":0.9958000183105469,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9916999936103821,"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/computer-science","display_name":"Computer science","score":0.7838881015777588},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6764061450958252},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6320297718048096},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5859926342964172},{"id":"https://openalex.org/keywords/hyperparameter","display_name":"Hyperparameter","score":0.5316484570503235},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4857388138771057},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4582502245903015},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.43933409452438354}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7838881015777588},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6764061450958252},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6320297718048096},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5859926342964172},{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.5316484570503235},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4857388138771057},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4582502245903015},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.43933409452438354},{"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/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":12,"locations":[{"id":"doi:10.1021/acs.jcim.9b01053","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01053","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.9b01053","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:32243153","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32243153","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},{"id":"pmh:oai:arXiv.org:1911.05211","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1911.05211","pdf_url":"https://arxiv.org/pdf/1911.05211","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"mag:2982872869","is_oa":true,"landing_page_url":"http://export.arxiv.org/pdf/1911.05211","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"pmh:oai:figshare.com:article/12137388","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/AMPL_A_Data-Driven_Modeling_Pipeline_for_Drug_Discovery/12137388","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:figshare.com:article/12137391","is_oa":true,"landing_page_url":"https://figshare.com/articles/AMPL_A_Data-Driven_Modeling_Pipeline_for_Drug_Discovery/12137391","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/12574040","is_oa":true,"landing_page_url":"https://figshare.com/articles/online_resource/AMPL_A_Data-Driven_Modeling_Pipeline_for_Drug_Discovery/12574040","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:osti.gov:1615090","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1615090","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:1616247","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1616247","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:1810633","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1810633","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7189366","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7189366","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},{"id":"doi:10.48550/arxiv.1911.05211","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1911.05211","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.9b01053","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01053","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.9b01053","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1234541941","display_name":null,"funder_award_id":"75N91019D00024","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4689185066","display_name":null,"funder_award_id":"75N91019D00024","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6252953675","display_name":null,"funder_award_id":"75N91019D00024","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"}],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320307773","display_name":"GlaxoSmithKline","ror":"https://ror.org/01xsqw823"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332369","display_name":"National Nuclear Security Administration","ror":"https://ror.org/03sk1we31"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320338286","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2982872869.pdf"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1835740130","https://openalex.org/W1988037271","https://openalex.org/W2076498053","https://openalex.org/W2101234009","https://openalex.org/W2290847742","https://openalex.org/W2295598076","https://openalex.org/W2594183968","https://openalex.org/W2777884179","https://openalex.org/W2791355014","https://openalex.org/W2803094965","https://openalex.org/W2806547269","https://openalex.org/W2889326414","https://openalex.org/W2950517871","https://openalex.org/W2966357564","https://openalex.org/W3102476541","https://openalex.org/W6930906673"],"related_works":["https://openalex.org/W2972518327","https://openalex.org/W2614986686","https://openalex.org/W2341150241","https://openalex.org/W2949262520","https://openalex.org/W3014157798","https://openalex.org/W3037161253","https://openalex.org/W3193587716","https://openalex.org/W3043318404","https://openalex.org/W3190938993","https://openalex.org/W2786676889","https://openalex.org/W2740519124","https://openalex.org/W2953333044","https://openalex.org/W3159567283","https://openalex.org/W2295562558","https://openalex.org/W2903318201","https://openalex.org/W3135043447","https://openalex.org/W2963198001","https://openalex.org/W3155456206","https://openalex.org/W2179966432","https://openalex.org/W3206292363"],"abstract_inverted_index":{"One":[0],"of":[1,20,61,71,85,93],"the":[2,11,21,59,62,123,153],"key":[3,49,96],"requirements":[4],"for":[5,41,155],"incorporating":[6],"machine":[7],"learning":[8],"(ML)":[9],"into":[10],"drug":[12],"discovery":[13],"process":[14],"is":[15,174],"complete":[16],"traceability":[17],"and":[18,24,37,43,67,73,146,170,177],"reproducibility":[19],"model":[22,135,147,165],"building":[23,42,166],"evaluation":[25],"process.":[26],"With":[27],"this":[28],"in":[29],"mind,":[30],"we":[31],"have":[32,78],"developed":[33],"an":[34,69,156],"end-to-end":[35],"modular":[36],"extensible":[38,157],"software":[39,173],"pipeline":[40,158],"sharing":[44],"ML":[45,72],"models":[46],"that":[47,99,111,159],"predict":[48,134],"pharma-relevant":[50],"parameters.":[51,94],"The":[52],"ATOM":[53],"Modeling":[54],"PipeLine,":[55],"or":[56],"AMPL,":[57],"extends":[58],"functionality":[60],"open":[63,175],"source":[64,176],"library":[65],"DeepChem":[66],"supports":[68],"array":[70],"molecular":[74,101],"featurization":[75],"tools.":[76],"We":[77,108],"benchmarked":[79],"AMPL":[80],"on":[81],"a":[82,90],"large":[83],"collection":[84],"pharmaceutical":[86],"data":[87,112,128,144],"sets":[88,145],"covering":[89],"wide":[91],"range":[92],"Our":[95,149],"findings":[97,150],"indicate":[98],"traditional":[100],"fingerprints":[102],"underperform":[103],"other":[104],"feature":[105],"representation":[106],"methods.":[107],"also":[109],"find":[110],"set":[113],"size":[114],"correlates":[115],"directly":[116],"with":[117,139],"prediction":[118],"performance,":[119],"which":[120],"points":[121],"to":[122,125,152,163],"need":[124,154],"expand":[126],"public":[127],"sets.":[129],"Uncertainty":[130],"quantification":[131],"can":[132,160],"help":[133],"error,":[136],"but":[137],"correlation":[138],"error":[140],"varies":[141],"considerably":[142],"between":[143],"types.":[148],"point":[151],"be":[161],"shared":[162],"make":[164],"more":[167],"widely":[168],"accessible":[169],"reproducible.":[171],"This":[172],"available":[178],"at:":[179],"https://github.com/ATOMconsortium/AMPL.":[180]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2025-10-10T00:00:00"}
