{"id":"https://openalex.org/W4387051186","doi":"https://doi.org/10.1186/s13321-023-00761-5","title":"A molecule perturbation software library and its application to study the effects of molecular design constraints","display_name":"A molecule perturbation software library and its application to study the effects of molecular design constraints","publication_year":2023,"publication_date":"2023-09-26","ids":{"openalex":"https://openalex.org/W4387051186","doi":"https://doi.org/10.1186/s13321-023-00761-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/37752561"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-023-00761-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00761-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00761-5","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/s13321-023-00761-5","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":["Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitslaan 1, 2610, Wilrijk, Belgium"],"affiliations":[{"raw_affiliation_string":"Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitslaan 1, 2610, Wilrijk, Belgium","institution_ids":["https://openalex.org/I149213910"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048522237","display_name":"Hans De Winter","orcid":"https://orcid.org/0000-0002-4450-7677"},"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":["Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitslaan 1, 2610, Wilrijk, Belgium. hans.dewinter@uantwerpen.be","Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitslaan 1, 2610, Wilrijk, Belgium"],"affiliations":[{"raw_affiliation_string":"Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitslaan 1, 2610, Wilrijk, Belgium. hans.dewinter@uantwerpen.be","institution_ids":[]},{"raw_affiliation_string":"Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitslaan 1, 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":0.5838,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.71724916,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":96},"biblio":{"volume":"15","issue":"1","first_page":"89","last_page":"89"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"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":0.9997000098228455,"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/T13180","display_name":"Chemistry and Chemical Engineering","score":0.9800999760627747,"subfield":{"id":"https://openalex.org/subfields/2304","display_name":"Environmental Chemistry"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9710000157356262,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6456557512283325},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5620875358581543},{"id":"https://openalex.org/keywords/perturbation","display_name":"Perturbation (astronomy)","score":0.5256541967391968},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.41966119408607483},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3907191753387451},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3709557056427002},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.33306053280830383},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17349377274513245},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10635256767272949}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6456557512283325},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5620875358581543},{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.5256541967391968},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.41966119408607483},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3907191753387451},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3709557056427002},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.33306053280830383},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17349377274513245},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10635256767272949},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13321-023-00761-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00761-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00761-5","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:37752561","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37752561","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:pubmedcentral.nih.gov:10523775","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10523775","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10523775/pdf/13321_2023_Article_761.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 Cheminform","raw_type":"Text"},{"id":"pmh:c:irua:199013","is_oa":false,"landing_page_url":"https://hdl.handle.net/10067/1990130151162165141","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:5a0f4476daa64208839be3909a3018f9","is_oa":true,"landing_page_url":"https://doaj.org/article/5a0f4476daa64208839be3909a3018f9","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-17 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-023-00761-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00761-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00761-5","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":"Partnerships for the goals","score":0.4000000059604645,"id":"https://metadata.un.org/sdg/17"}],"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":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387051186.pdf"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1591078033","https://openalex.org/W1592238003","https://openalex.org/W1754042689","https://openalex.org/W1968217405","https://openalex.org/W1972978214","https://openalex.org/W1974673082","https://openalex.org/W1982682305","https://openalex.org/W1988037271","https://openalex.org/W1991286793","https://openalex.org/W1991615245","https://openalex.org/W1999738209","https://openalex.org/W2012757283","https://openalex.org/W2012971387","https://openalex.org/W2022476850","https://openalex.org/W2025948031","https://openalex.org/W2032924120","https://openalex.org/W2034549041","https://openalex.org/W2037586880","https://openalex.org/W2038702914","https://openalex.org/W2041282815","https://openalex.org/W2041686943","https://openalex.org/W2052933929","https://openalex.org/W2096541451","https://openalex.org/W2107160601","https://openalex.org/W2110791536","https://openalex.org/W2125426232","https://openalex.org/W2151074799","https://openalex.org/W2160592148","https://openalex.org/W2170082200","https://openalex.org/W2294798173","https://openalex.org/W2412446857","https://openalex.org/W2578240541","https://openalex.org/W2594328795","https://openalex.org/W2599156179","https://openalex.org/W2610148085","https://openalex.org/W2900694120","https://openalex.org/W2909063104","https://openalex.org/W2952497504","https://openalex.org/W2953128081","https://openalex.org/W3014154196","https://openalex.org/W3023600056","https://openalex.org/W3045153201","https://openalex.org/W3078129399","https://openalex.org/W3087570960","https://openalex.org/W3094640617","https://openalex.org/W3116865743","https://openalex.org/W3165171933","https://openalex.org/W3208515103","https://openalex.org/W3213354351","https://openalex.org/W4206107836","https://openalex.org/W4245443308","https://openalex.org/W4253980551","https://openalex.org/W4307468223","https://openalex.org/W4319986489"],"related_works":["https://openalex.org/W2382940112","https://openalex.org/W2900071958","https://openalex.org/W2366131202","https://openalex.org/W2064192375","https://openalex.org/W1977631941","https://openalex.org/W2003249119","https://openalex.org/W2390280617","https://openalex.org/W2390634895","https://openalex.org/W1974311322","https://openalex.org/W2149263892"],"abstract_inverted_index":{"Computational":[0],"molecular":[1,99,124],"design":[2],"can":[3,127],"yield":[4],"chemically":[5,49],"unreasonable":[6],"compounds":[7],"when":[8],"performed":[9],"carelessly.":[10],"A":[11],"popular":[12],"strategy":[13],"to":[14,116],"mitigate":[15],"this":[16,63],"risk":[17],"is":[18,23,39],"mimicking":[19,88],"reference":[20,89],"chemistry.":[21],"This":[22],"commonly":[24],"achieved":[25],"by":[26,79],"restricting":[27,98,123],"the":[28,103],"way":[29],"in":[30,47],"which":[31],"molecules":[32,87],"are":[33],"constructed":[34],"or":[35],"modified.":[36],"While":[37],"it":[38],"well":[40],"established":[41],"that":[42,97],"such":[43],"an":[44],"approach":[45],"helps":[46],"designing":[48],"appealing":[50],"molecules,":[51,113],"concerns":[52],"about":[53],"these":[54],"restrictions":[55],"impacting":[56],"chemical":[57,90,120,131],"space":[58,132],"exploration":[59],"negatively":[60],"linger.":[61],"In":[62],"work":[64],"we":[65],"present":[66],"a":[67,81],"software":[68],"library":[69],"for":[70],"constrained":[71],"graph-based":[72],"molecule":[73,82],"manipulation":[74],"and":[75,109],"showcase":[76],"its":[77],"functionality":[78],"developing":[80],"generator.":[83],"Said":[84],"generator":[85],"designs":[86],"features":[91],"of":[92,111],"differing":[93],"granularity.":[94],"We":[95],"find":[96],"construction":[100,125],"lightly,":[101],"beyond":[102],"usual":[104],"positive":[105],"effects":[106],"on":[107],"drug-likeness":[108],"synthesizability":[110],"designed":[112],"provides":[114],"guidance":[115],"optimization":[117],"algorithms":[118],"navigating":[119],"space.":[121],"Nonetheless,":[122],"excessively":[126],"indeed":[128],"hinder":[129],"effective":[130],"exploration.":[133]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}