{"id":"https://openalex.org/W4206107836","doi":"https://doi.org/10.1186/s13321-022-00582-y","title":"LEADD: Lamarckian evolutionary algorithm for de novo drug design","display_name":"LEADD: Lamarckian evolutionary algorithm for de novo drug design","publication_year":2022,"publication_date":"2022-01-15","ids":{"openalex":"https://openalex.org/W4206107836","doi":"https://doi.org/10.1186/s13321-022-00582-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/35033209"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-022-00582-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00582-y","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00582-y","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/s13321-022-00582-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080600956","display_name":"Alan Kerstjens","orcid":null},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Alan Kerstjens","raw_affiliation_strings":["Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1A, 2610, Wilrijk, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1A, 2610, Wilrijk, Belgium","institution_ids":["https://openalex.org/I149213910"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048522237","display_name":"Hans De Winter","orcid":null},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Hans De Winter","raw_affiliation_strings":["Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1A, 2610, Wilrijk, Belgium. hans.dewinter@uantwerpen.be","Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1A, 2610, Wilrijk, Belgium"],"raw_orcid":"https://orcid.org/0000-0002-4450-7677","affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1A, 2610, Wilrijk, Belgium. hans.dewinter@uantwerpen.be","institution_ids":["https://openalex.org/I149213910"]},{"raw_affiliation_string":"Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1A, 2610, Wilrijk, Belgium","institution_ids":["https://openalex.org/I149213910"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5080600956"],"corresponding_institution_ids":["https://openalex.org/I149213910"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":5.1805,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.95994742,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"14","issue":"1","first_page":"3","last_page":"3"},"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/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9283000230789185,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11053","display_name":"Process Optimization and Integration","score":0.9110999703407288,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7151068449020386},{"id":"https://openalex.org/keywords/evolutionary-algorithm","display_name":"Evolutionary algorithm","score":0.5834854245185852},{"id":"https://openalex.org/keywords/chemical-space","display_name":"Chemical space","score":0.4704046845436096},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.44551706314086914},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.43700164556503296},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3840939998626709},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.3425455689430237},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3272641897201538},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1842505931854248}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7151068449020386},{"id":"https://openalex.org/C159149176","wikidata":"https://www.wikidata.org/wiki/Q14489129","display_name":"Evolutionary algorithm","level":2,"score":0.5834854245185852},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.4704046845436096},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.44551706314086914},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.43700164556503296},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3840939998626709},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3425455689430237},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3272641897201538},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1842505931854248},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13321-022-00582-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00582-y","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00582-y","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:35033209","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35033209","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:c:irua:184632","is_oa":false,"landing_page_url":"https://hdl.handle.net/10067/1846320151162165141","pdf_url":null,"source":{"id":"https://openalex.org/S4306401849","display_name":"Institutional Repository University of Antwerp (University of Antwerp)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149213910","host_organization_name":"University of Antwerp","host_organization_lineage":["https://openalex.org/I149213910"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:doaj.org/article:4d5d928541ca4af8974bddaefb6e9351","is_oa":true,"landing_page_url":"https://doaj.org/article/4d5d928541ca4af8974bddaefb6e9351","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 14, Iss 1, Pp 1-20 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8760751","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8760751","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/s13321-022-00582-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00582-y","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00582-y","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":[],"awards":[{"id":"https://openalex.org/G1226304562","display_name":null,"funder_award_id":"39461","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320319128","display_name":"Vlaams Supercomputer Centrum","ror":null},{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320327336","display_name":"Vlaamse regering","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4206107836.pdf","grobid_xml":"https://content.openalex.org/works/W4206107836.grobid-xml"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W1174108660","https://openalex.org/W1549148204","https://openalex.org/W1562424368","https://openalex.org/W1592238003","https://openalex.org/W1757990252","https://openalex.org/W1964183799","https://openalex.org/W1972978214","https://openalex.org/W1974419458","https://openalex.org/W1979278760","https://openalex.org/W1983439863","https://openalex.org/W1988037271","https://openalex.org/W2004797093","https://openalex.org/W2017254234","https://openalex.org/W2023818227","https://openalex.org/W2027065525","https://openalex.org/W2027478081","https://openalex.org/W2032924120","https://openalex.org/W2037586880","https://openalex.org/W2041282815","https://openalex.org/W2041686943","https://openalex.org/W2044834685","https://openalex.org/W2047819524","https://openalex.org/W2052933929","https://openalex.org/W2075307413","https://openalex.org/W2078048835","https://openalex.org/W2096541451","https://openalex.org/W2097446729","https://openalex.org/W2107160601","https://openalex.org/W2110791536","https://openalex.org/W2113863960","https://openalex.org/W2114704115","https://openalex.org/W2121853844","https://openalex.org/W2146984355","https://openalex.org/W2160592148","https://openalex.org/W2166478947","https://openalex.org/W2247581895","https://openalex.org/W2325619789","https://openalex.org/W2325811289","https://openalex.org/W2330173753","https://openalex.org/W2396663079","https://openalex.org/W2529996553","https://openalex.org/W2536967169","https://openalex.org/W2747592475","https://openalex.org/W2770765812","https://openalex.org/W2805002767","https://openalex.org/W2900694120","https://openalex.org/W2914542247","https://openalex.org/W2951739446","https://openalex.org/W2952497504","https://openalex.org/W2953128081","https://openalex.org/W2999242200","https://openalex.org/W3014154196","https://openalex.org/W3024423177","https://openalex.org/W3030402150","https://openalex.org/W3098269892","https://openalex.org/W3101155908","https://openalex.org/W4245443308"],"related_works":["https://openalex.org/W2973074952","https://openalex.org/W2726551571","https://openalex.org/W4283395020","https://openalex.org/W4320732452","https://openalex.org/W135095951","https://openalex.org/W4286980196","https://openalex.org/W4385588199","https://openalex.org/W3199987505","https://openalex.org/W4385760073","https://openalex.org/W2600435468"],"abstract_inverted_index":{"Given":[0],"an":[1],"objective":[2,28],"function":[3],"that":[4,23,38,99,134,158],"predicts":[5],"key":[6],"properties":[7],"of":[8,34,72,82,92,115,131,163],"a":[9,17,31,51,65,139,154,175,180],"molecule,":[10],"goal-directed":[11],"de":[12,56],"novo":[13,57],"molecular":[14,93],"design":[15,42,59],"is":[16,37,118,143],"useful":[18],"tool":[19],"to":[20,41,63,120,169,187,190,202,205],"identify":[21,191],"molecules":[22,74,89,117,193,199],"maximize":[24],"or":[25],"minimize":[26],"said":[27],"function.":[29],"Nonetheless,":[30],"common":[32],"drawback":[33],"these":[35,136],"methods":[36],"they":[39],"tend":[40],"synthetically":[43,84],"unfeasible":[44],"molecules.":[45,164],"In":[46],"this":[47],"paper":[48],"we":[49,151],"describe":[50],"Lamarckian":[52,155],"evolutionary":[53,156,177,212],"algorithm":[54,178],"for":[55],"drug":[58],"(LEADD).":[60],"LEADD":[61,87,165],"attempts":[62],"strike":[64],"balance":[66],"between":[67,103],"optimization":[68],"power,":[69],"synthetic":[70],"accessibility":[71],"designed":[73,198,209],"and":[75,95,125,174,184],"computational":[76],"efficiency.":[77],"To":[78,145],"increase":[79],"the":[80,97,160,197],"likelihood":[81],"designing":[83],"accessible":[85],"molecules,":[86],"represents":[88],"as":[90],"graphs":[91],"fragments,":[94,122],"limits":[96],"bonds":[98],"can":[100],"be":[101,188,203],"formed":[102],"them":[104],"through":[105],"knowledge-based":[106],"pairwise":[107],"atom":[108],"type":[109],"compatibility":[110,126],"rules.":[111,127],"A":[112,128],"reference":[113],"library":[114],"drug-like":[116],"used":[119],"extract":[121],"fragment":[123],"preferences":[124],"novel":[129],"set":[130],"genetic":[132],"operators":[133],"enforce":[135],"rules":[137],"in":[138],"computationally":[140],"efficient":[141],"manner":[142],"presented.":[144],"sample":[146],"chemical":[147],"space":[148],"more":[149,194],"efficiently":[150],"also":[152],"explore":[153],"mechanism":[157],"adapts":[159],"reproductive":[161],"behavior":[162],"has":[166],"been":[167],"compared":[168],"both":[170],"standard":[171],"virtual":[172],"screening":[173],"comparable":[176],"using":[179],"standardized":[181],"benchmark":[182],"suite":[183],"was":[185],"shown":[186],"able":[189],"fitter":[192],"efficiently.":[195],"Moreover,":[196],"are":[200],"predicted":[201],"easier":[204],"synthesize":[206],"than":[207],"those":[208],"by":[210],"other":[211],"algorithms.":[213]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":5}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
