{"id":"https://openalex.org/W3024423177","doi":"https://doi.org/10.1186/s13321-020-00429-4","title":"AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization","display_name":"AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization","publication_year":2020,"publication_date":"2020-04-17","ids":{"openalex":"https://openalex.org/W3024423177","doi":"https://doi.org/10.1186/s13321-020-00429-4","mag":"3024423177","pmid":"https://pubmed.ncbi.nlm.nih.gov/33431021"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-020-00429-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00429-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-020-00429-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"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 Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-020-00429-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031636174","display_name":"Jacob O. Spiegel","orcid":"https://orcid.org/0000-0002-8496-6915"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob O. Spiegel","raw_affiliation_strings":["Department of Biological Sciences, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084976210","display_name":"Jacob D. Durrant","orcid":"https://orcid.org/0000-0002-5808-4097"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jacob D. Durrant","raw_affiliation_strings":["Department of Biological Sciences, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA. durrantj@pitt.edu","Department of Biological Sciences, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA. durrantj@pitt.edu","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5084976210"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":8.3512,"has_fulltext":true,"cited_by_count":183,"citation_normalized_percentile":{"value":0.9831544,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"12","issue":"1","first_page":"25","last_page":"25"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11914","display_name":"PARP inhibition in cancer therapy","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11914","display_name":"PARP inhibition in cancer therapy","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9879999756813049,"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/T10123","display_name":"DNA Repair Mechanisms","score":0.9546999931335449,"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/cheminformatics","display_name":"Cheminformatics","score":0.8175516128540039},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7001813650131226},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5391320586204529},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.5058678984642029},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.5035373568534851},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48541459441185},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4758843183517456},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.46493643522262573},{"id":"https://openalex.org/keywords/binding-affinities","display_name":"Binding affinities","score":0.41916772723197937},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.3827597498893738},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3470463752746582},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19826331734657288},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1479511260986328},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14143359661102295},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.14017513394355774},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.09831452369689941}],"concepts":[{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.8175516128540039},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7001813650131226},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5391320586204529},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5058678984642029},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.5035373568534851},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48541459441185},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4758843183517456},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.46493643522262573},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.41916772723197937},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.3827597498893738},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3470463752746582},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19826331734657288},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1479511260986328},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14143359661102295},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.14017513394355774},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.09831452369689941},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-020-00429-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00429-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-020-00429-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"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 Cheminformatics","raw_type":"journal-article"},{"id":"pmid:33431021","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33431021","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 cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:7cce4e0db5d64d7e83f78e6dc9d1c40e","is_oa":true,"landing_page_url":"https://doaj.org/article/7cce4e0db5d64d7e83f78e6dc9d1c40e","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 12, Iss 1, Pp 1-16 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7165399","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7165399","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-020-00429-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00429-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-020-00429-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"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 Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.4099999964237213}],"awards":[],"funders":[{"id":"https://openalex.org/F4320310174","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3024423177.pdf","grobid_xml":"https://content.openalex.org/works/W3024423177.grobid-xml"},"referenced_works_count":112,"referenced_works":["https://openalex.org/W257686297","https://openalex.org/W987011638","https://openalex.org/W1499536210","https://openalex.org/W1509196567","https://openalex.org/W1582109070","https://openalex.org/W1757990252","https://openalex.org/W1931417114","https://openalex.org/W1968997369","https://openalex.org/W1970544425","https://openalex.org/W1978222579","https://openalex.org/W1984994707","https://openalex.org/W1986804628","https://openalex.org/W1989136612","https://openalex.org/W1992947643","https://openalex.org/W1993285168","https://openalex.org/W1995343013","https://openalex.org/W2004797093","https://openalex.org/W2010339813","https://openalex.org/W2010795100","https://openalex.org/W2011230643","https://openalex.org/W2011301426","https://openalex.org/W2011647105","https://openalex.org/W2014035465","https://openalex.org/W2016294484","https://openalex.org/W2017254234","https://openalex.org/W2017575881","https://openalex.org/W2022476850","https://openalex.org/W2023818227","https://openalex.org/W2025572488","https://openalex.org/W2030286884","https://openalex.org/W2032924120","https://openalex.org/W2033016300","https://openalex.org/W2037825667","https://openalex.org/W2038935913","https://openalex.org/W2041040308","https://openalex.org/W2041767096","https://openalex.org/W2042572511","https://openalex.org/W2043509228","https://openalex.org/W2047399603","https://openalex.org/W2047544230","https://openalex.org/W2050440510","https://openalex.org/W2050458179","https://openalex.org/W2052907531","https://openalex.org/W2058686370","https://openalex.org/W2078521274","https://openalex.org/W2080618096","https://openalex.org/W2085215116","https://openalex.org/W2095798342","https://openalex.org/W2096136751","https://openalex.org/W2096864392","https://openalex.org/W2097446729","https://openalex.org/W2101368370","https://openalex.org/W2105664288","https://openalex.org/W2105668062","https://openalex.org/W2107160601","https://openalex.org/W2108389384","https://openalex.org/W2112411768","https://openalex.org/W2113364934","https://openalex.org/W2113580085","https://openalex.org/W2113863960","https://openalex.org/W2124072633","https://openalex.org/W2127553917","https://openalex.org/W2127957276","https://openalex.org/W2134967712","https://openalex.org/W2135409663","https://openalex.org/W2135732933","https://openalex.org/W2137755195","https://openalex.org/W2139614856","https://openalex.org/W2144135270","https://openalex.org/W2148628152","https://openalex.org/W2151697120","https://openalex.org/W2155063687","https://openalex.org/W2165168652","https://openalex.org/W2165565773","https://openalex.org/W2166478947","https://openalex.org/W2169678694","https://openalex.org/W2177419974","https://openalex.org/W2209979687","https://openalex.org/W2269471019","https://openalex.org/W2270704840","https://openalex.org/W2294932319","https://openalex.org/W2396663079","https://openalex.org/W2529759555","https://openalex.org/W2531370029","https://openalex.org/W2554099577","https://openalex.org/W2557144746","https://openalex.org/W2557717244","https://openalex.org/W2609026834","https://openalex.org/W2610148085","https://openalex.org/W2614952490","https://openalex.org/W2740934820","https://openalex.org/W2755668533","https://openalex.org/W2759783782","https://openalex.org/W2761228804","https://openalex.org/W2765932489","https://openalex.org/W2784007709","https://openalex.org/W2796717827","https://openalex.org/W2798613236","https://openalex.org/W2902625972","https://openalex.org/W2902946687","https://openalex.org/W2914635984","https://openalex.org/W2917732060","https://openalex.org/W2920724574","https://openalex.org/W2937816774","https://openalex.org/W2943789407","https://openalex.org/W2947285137","https://openalex.org/W3006759222","https://openalex.org/W3007133919","https://openalex.org/W3106536628","https://openalex.org/W4248107770","https://openalex.org/W4285719527","https://openalex.org/W6601846001"],"related_works":["https://openalex.org/W4362464865","https://openalex.org/W2098840560","https://openalex.org/W2768880727","https://openalex.org/W2773493604","https://openalex.org/W2621548818","https://openalex.org/W2113146994","https://openalex.org/W2269591907","https://openalex.org/W2073081213","https://openalex.org/W2027065525","https://openalex.org/W4302604134"],"abstract_inverted_index":{"We":[0],"here":[1,99],"present":[2],"AutoGrow4,":[3],"an":[4],"open-source":[5],"program":[6],"for":[7,40,47],"semi-automated":[8],"computer-aided":[9],"drug":[10],"discovery.":[11],"AutoGrow4":[12,58,101,116,137,147,154],"uses":[13],"a":[14,29,37,83,111],"genetic":[15],"algorithm":[16],"to":[17,28,81,102],"evolve":[18],"predicted":[19,122,132],"ligands":[20],"on":[21],"demand":[22],"and":[23,46,55,63,78,95],"so":[24],"is":[25,36,59,148,155],"not":[26],"limited":[27],"virtual":[30],"library":[31],"of":[32,86,106,135,141,160,172],"pre-enumerated":[33],"compounds.":[34],"It":[35,69],"useful":[38],"tool":[39],"generating":[41],"entirely":[42],"novel":[43],"drug-like":[44,118],"molecules":[45],"optimizing":[48],"preexisting":[49],"ligands.":[50],"By":[51],"leveraging":[52],"recent":[53],"computational":[54],"cheminformatics":[56],"advancements,":[57],"faster,":[60],"more":[61,64],"stable,":[62],"modular":[65],"than":[66,125],"previous":[67],"versions.":[68],"implements":[70],"new":[71],"docking-program":[72],"compatibility,":[73],"chemical":[74],"filters,":[75],"multithreading":[76],"options,":[77],"selection":[79],"methods":[80],"support":[82],"wide":[84],"range":[85],"user":[87],"needs.":[88],"To":[89],"illustrate":[90],"both":[91],"de":[92],"novo":[93],"design":[94],"lead":[96],"optimization,":[97],"we":[98],"apply":[100],"the":[103,136,142,158,161],"catalytic":[104],"domain":[105],"poly(ADP-ribose)":[107],"polymerase":[108],"1":[109],"(PARP-1),":[110],"well":[112],"characterized":[113],"DNA-damage-recognition":[114],"protein.":[115],"produces":[117],"compounds":[119,138],"with":[120,150],"better":[121],"binding":[123,133],"affinities":[124],"FDA-approved":[126],"PARP-1":[127],"inhibitors":[128],"(positive":[129],"controls).":[130],"The":[131],"modes":[134],"mimic":[139],"those":[140],"known":[143],"inhibitors,":[144],"even":[145],"when":[146],"seeded":[149],"random":[151],"small":[152],"molecules.":[153],"available":[156],"under":[157],"terms":[159],"Apache":[162],"License,":[163],"Version":[164],"2.0.":[165],"A":[166],"copy":[167],"can":[168],"be":[169],"downloaded":[170],"free":[171],"charge":[173],"from":[174],"http://durrantlab.com/autogrow4.":[175]},"counts_by_year":[{"year":2026,"cited_by_count":14},{"year":2025,"cited_by_count":39},{"year":2024,"cited_by_count":38},{"year":2023,"cited_by_count":38},{"year":2022,"cited_by_count":20},{"year":2021,"cited_by_count":31},{"year":2020,"cited_by_count":3}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}