{"id":"https://openalex.org/W4390755655","doi":"https://doi.org/10.1021/acs.jcim.3c01406","title":"DockOpt: A Tool for Automatic Optimization of Docking Models","display_name":"DockOpt: A Tool for Automatic Optimization of Docking Models","publication_year":2024,"publication_date":"2024-01-11","ids":{"openalex":"https://openalex.org/W4390755655","doi":"https://doi.org/10.1021/acs.jcim.3c01406","pmid":"https://pubmed.ncbi.nlm.nih.gov/38206771"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c01406","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01406","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c01406","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c01406","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017231621","display_name":"Ian Knight","orcid":null},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ian S. Knight","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071344692","display_name":"Olivier Mailhot","orcid":"https://orcid.org/0000-0002-7533-4561"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Olivier Mailhot","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090904857","display_name":"Khanh Tang","orcid":null},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Khanh G. Tang","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054045417","display_name":"John J. Irwin","orcid":"https://orcid.org/0000-0002-1195-6417"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John J. Irwin","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States"],"raw_orcid":"https://orcid.org/0000-0002-1195-6417","affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States","institution_ids":["https://openalex.org/I180670191"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5054045417"],"corresponding_institution_ids":["https://openalex.org/I180670191"],"apc_list":null,"apc_paid":null,"fwci":1.3523,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.80865511,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"64","issue":"3","first_page":"1004","last_page":"1016"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994000196456909,"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":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9944000244140625,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9937999844551086,"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/dock","display_name":"DOCK","score":0.9243790507316589},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.7123037576675415},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6873738765716553},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6666440963745117},{"id":"https://openalex.org/keywords/automation","display_name":"Automation","score":0.4923297166824341},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.4714827537536621},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.4485442042350769},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3920424282550812},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3457793593406677},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3314518928527832},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.2808673083782196},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.22869104146957397},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2056145966053009},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.12096986174583435},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09878727793693542},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.06464383006095886}],"concepts":[{"id":"https://openalex.org/C93073132","wikidata":"https://www.wikidata.org/wiki/Q24726581","display_name":"DOCK","level":2,"score":0.9243790507316589},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7123037576675415},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6873738765716553},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6666440963745117},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.4923297166824341},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.4714827537536621},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.4485442042350769},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3920424282550812},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3457793593406677},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3314518928527832},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.2808673083782196},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.22869104146957397},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2056145966053009},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.12096986174583435},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09878727793693542},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.06464383006095886},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C199104240","wikidata":"https://www.wikidata.org/wiki/Q118291","display_name":"Marine engineering","level":1,"score":0.0}],"mesh":[{"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":"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":"D011446","descriptor_name":"Prospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011446","descriptor_name":"Prospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011446","descriptor_name":"Prospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011446","descriptor_name":"Prospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011446","descriptor_name":"Prospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011446","descriptor_name":"Prospective Studies","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":"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":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.3c01406","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01406","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c01406","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:38206771","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38206771","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:escholarship.org:ark:/13030/qt37c6g7mv","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/37c6g7mv","pdf_url":"https://escholarship.org/content/qt37c6g7mv/qt37c6g7mv.pdf?t=sg3ir7","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Chemical Information and Modeling, vol 64, iss 3","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10865354","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10865354","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10865354/pdf/ci3c01406.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.3c01406","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01406","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c01406","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4099999964237213,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1890007942","display_name":null,"funder_award_id":"GM133836","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G653760849","display_name":null,"funder_award_id":"GM133836","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390755655.pdf","grobid_xml":"https://content.openalex.org/works/W4390755655.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1983376893","https://openalex.org/W2000350990","https://openalex.org/W2007249694","https://openalex.org/W2055043387","https://openalex.org/W2058120003","https://openalex.org/W2058835307","https://openalex.org/W2061745280","https://openalex.org/W2089188080","https://openalex.org/W2099900074","https://openalex.org/W2101078720","https://openalex.org/W2124074156","https://openalex.org/W2132629607","https://openalex.org/W2134334341","https://openalex.org/W2134967712","https://openalex.org/W2135274037","https://openalex.org/W2429079944","https://openalex.org/W2521868064","https://openalex.org/W2883755802","https://openalex.org/W2912171584","https://openalex.org/W2932935282","https://openalex.org/W2983225234","https://openalex.org/W2996206630","https://openalex.org/W3004731690","https://openalex.org/W3005417975","https://openalex.org/W3010016408","https://openalex.org/W3024763884","https://openalex.org/W3036674808","https://openalex.org/W3108778136","https://openalex.org/W3120407713","https://openalex.org/W3126031592","https://openalex.org/W3135726897","https://openalex.org/W3165388098","https://openalex.org/W3168430821","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3199633702","https://openalex.org/W3201539868","https://openalex.org/W3209170263","https://openalex.org/W3212543990","https://openalex.org/W3213381480","https://openalex.org/W3214341251","https://openalex.org/W4200233821","https://openalex.org/W4200289210","https://openalex.org/W4206509885","https://openalex.org/W4206924409","https://openalex.org/W4210617107","https://openalex.org/W4211232835","https://openalex.org/W4229037605","https://openalex.org/W4280552582","https://openalex.org/W4297497355","https://openalex.org/W4297995910","https://openalex.org/W4307074410","https://openalex.org/W4311612485","https://openalex.org/W4313484931","https://openalex.org/W4366241519","https://openalex.org/W4379967278"],"related_works":["https://openalex.org/W4282913408","https://openalex.org/W2057846043","https://openalex.org/W2336040088","https://openalex.org/W4393853640","https://openalex.org/W2100436540","https://openalex.org/W3193731429","https://openalex.org/W2027065525","https://openalex.org/W2149658535","https://openalex.org/W2750247885","https://openalex.org/W2773493604"],"abstract_inverted_index":{"Molecular":[0],"docking":[1,34,50,68],"is":[2,121,138],"a":[3,43,55],"widely":[4],"used":[5],"technique":[6],"for":[7,11,98,140,149],"leveraging":[8],"protein":[9],"structure":[10],"ligand":[12],"discovery,":[13],"but":[14],"it":[15],"remains":[16],"difficult":[17],"to":[18,21,71,105,142],"utilize":[19],"due":[20],"limitations":[22],"that":[23],"have":[24],"not":[25],"been":[26],"adequately":[27],"addressed.":[28],"Despite":[29],"some":[30],"progress":[31],"toward":[32],"automation,":[33],"still":[35],"requires":[36],"expert":[37],"guidance,":[38],"hindering":[39],"its":[40],"adoption":[41],"by":[42],"broader":[44],"range":[45],"of":[46,67,100,116,125],"investigators.":[47],"To":[48],"make":[49],"more":[51],"accessible,":[52],"we":[53],"developed":[54],"new":[56],"utility":[57],"called":[58],"DockOpt,":[59],"which":[60,137],"automates":[61],"the":[62,89,95,126,132],"creation,":[63],"evaluation,":[64],"and":[65,94,147],"optimization":[66],"models":[69,97],"prior":[70],"their":[72,107],"deployment":[73],"in":[74,88,109,131],"large-scale":[75],"prospective":[76,110],"screens.":[77],"DockOpt":[78,120],"outperforms":[79],"our":[80],"previous":[81],"automated":[82],"pipeline":[83],"across":[84],"all":[85],"43":[86],"targets":[87,101],"DUDE-Z":[90],"benchmark":[91],"data":[92],"set,":[93],"generated":[96],"84%":[99],"demonstrate":[102],"sufficient":[103],"enrichment":[104],"warrant":[106],"use":[108],"screens,":[111],"with":[112],"normalized":[113],"LogAUC":[114],"values":[115],"at":[117,145,153],"least":[118],"15%.":[119],"available":[122,139],"as":[123],"part":[124],"Python":[127],"package":[128],"Pydock3":[129],"included":[130],"UCSF":[133],"DOCK":[134],"3.8":[135],"distribution,":[136],"free":[141,148],"academic":[143],"researchers":[144],"https://dock.compbio.ucsf.edu":[146],"everyone":[150],"upon":[151],"registration":[152],"https://tldr.docking.org.":[154]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-13T08:25:38.343686","created_date":"2025-10-10T00:00:00"}