{"id":"https://openalex.org/W3106065498","doi":"https://doi.org/10.1021/acs.jcim.0c00920","title":"Shape-Based Descriptors for Efficient Structure-Based Fragment Growing","display_name":"Shape-Based Descriptors for Efficient Structure-Based Fragment Growing","publication_year":2020,"publication_date":"2020-11-16","ids":{"openalex":"https://openalex.org/W3106065498","doi":"https://doi.org/10.1021/acs.jcim.0c00920","mag":"3106065498","pmid":"https://pubmed.ncbi.nlm.nih.gov/33196169"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00920","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00920","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045205619","display_name":"Patrick Penner","orcid":"https://orcid.org/0000-0003-4988-6183"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Patrick Penner","raw_affiliation_strings":["ZBH\u2212Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, 20146 Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-4988-6183","affiliations":[{"raw_affiliation_string":"ZBH\u2212Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061419406","display_name":"Virginie Martiny","orcid":"https://orcid.org/0000-0002-6866-3957"},"institutions":[{"id":"https://openalex.org/I4210135308","display_name":"Servier (France)","ror":"https://ror.org/034e7c066","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210135308"]},{"id":"https://openalex.org/I84909340","display_name":"Institut des Hautes \u00c9tudes Scientifiques","ror":"https://ror.org/05d5m2r55","country_code":"FR","type":"facility","lineage":["https://openalex.org/I84909340"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Virginie Martiny","raw_affiliation_strings":["Institut Recherches de Servier, 125 Chemin de Ronde, 78290 Croissy, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Recherches de Servier, 125 Chemin de Ronde, 78290 Croissy, France","institution_ids":["https://openalex.org/I84909340","https://openalex.org/I4210135308"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060277103","display_name":"Arnaud Gohier","orcid":null},"institutions":[{"id":"https://openalex.org/I4210135308","display_name":"Servier (France)","ror":"https://ror.org/034e7c066","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210135308"]},{"id":"https://openalex.org/I84909340","display_name":"Institut des Hautes \u00c9tudes Scientifiques","ror":"https://ror.org/05d5m2r55","country_code":"FR","type":"facility","lineage":["https://openalex.org/I84909340"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Arnaud Gohier","raw_affiliation_strings":["Institut Recherches de Servier, 125 Chemin de Ronde, 78290 Croissy, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Recherches de Servier, 125 Chemin de Ronde, 78290 Croissy, France","institution_ids":["https://openalex.org/I84909340","https://openalex.org/I4210135308"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045908044","display_name":"Marcus Gastreich","orcid":"https://orcid.org/0000-0001-5564-7117"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Marcus Gastreich","raw_affiliation_strings":["BioSolveIT GmbH, An der Ziegelei 79, 53757 Sankt Augustin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioSolveIT GmbH, An der Ziegelei 79, 53757 Sankt Augustin, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057496649","display_name":"Pierre Ducrot","orcid":"https://orcid.org/0000-0002-9868-5962"},"institutions":[{"id":"https://openalex.org/I4210135308","display_name":"Servier (France)","ror":"https://ror.org/034e7c066","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210135308"]},{"id":"https://openalex.org/I84909340","display_name":"Institut des Hautes \u00c9tudes Scientifiques","ror":"https://ror.org/05d5m2r55","country_code":"FR","type":"facility","lineage":["https://openalex.org/I84909340"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pierre Ducrot","raw_affiliation_strings":["Institut Recherches de Servier, 125 Chemin de Ronde, 78290 Croissy, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Recherches de Servier, 125 Chemin de Ronde, 78290 Croissy, France","institution_ids":["https://openalex.org/I84909340","https://openalex.org/I4210135308"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101866953","display_name":"David Brown","orcid":"https://orcid.org/0000-0002-7986-5052"},"institutions":[{"id":"https://openalex.org/I4210135308","display_name":"Servier (France)","ror":"https://ror.org/034e7c066","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210135308"]},{"id":"https://openalex.org/I84909340","display_name":"Institut des Hautes \u00c9tudes Scientifiques","ror":"https://ror.org/05d5m2r55","country_code":"FR","type":"facility","lineage":["https://openalex.org/I84909340"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"David Brown","raw_affiliation_strings":["Institut Recherches de Servier, 125 Chemin de Ronde, 78290 Croissy, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Recherches de Servier, 125 Chemin de Ronde, 78290 Croissy, France","institution_ids":["https://openalex.org/I84909340","https://openalex.org/I4210135308"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083205378","display_name":"Matthias Rarey","orcid":"https://orcid.org/0000-0002-9553-6531"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Matthias Rarey","raw_affiliation_strings":["ZBH\u2212Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, 20146 Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9553-6531","affiliations":[{"raw_affiliation_string":"ZBH\u2212Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5083205378"],"corresponding_institution_ids":["https://openalex.org/I159176309"],"apc_list":null,"apc_paid":null,"fwci":0.8738,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.80394513,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"60","issue":"12","first_page":"6269","last_page":"6281"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9987000226974487,"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":0.9987000226974487,"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":0.9979000091552734,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9937000274658203,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.9556698799133301},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7200394868850708},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6685876250267029},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5355923175811768},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3972049951553345},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36298245191574097},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.22424235939979553},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.15721666812896729}],"concepts":[{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.9556698799133301},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7200394868850708},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6685876250267029},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5355923175811768},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3972049951553345},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36298245191574097},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.22424235939979553},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.15721666812896729},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.0c00920","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00920","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:33196169","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33196169","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320327235","display_name":"Servier","ror":"https://ror.org/034e7c066"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1174108660","https://openalex.org/W1509196567","https://openalex.org/W1592238003","https://openalex.org/W1996100382","https://openalex.org/W2019504379","https://openalex.org/W2027065525","https://openalex.org/W2038617772","https://openalex.org/W2040154749","https://openalex.org/W2046258407","https://openalex.org/W2052933929","https://openalex.org/W2064514012","https://openalex.org/W2069152576","https://openalex.org/W2079804724","https://openalex.org/W2090936831","https://openalex.org/W2114779636","https://openalex.org/W2123058437","https://openalex.org/W2126823383","https://openalex.org/W2166704869","https://openalex.org/W2220825152","https://openalex.org/W2238707319","https://openalex.org/W2347697584","https://openalex.org/W2396663079","https://openalex.org/W2467779447","https://openalex.org/W2559603838","https://openalex.org/W2587598315","https://openalex.org/W2614021444","https://openalex.org/W2794774007","https://openalex.org/W2883435671","https://openalex.org/W2884441791","https://openalex.org/W2902812092","https://openalex.org/W2904240839","https://openalex.org/W2911847761","https://openalex.org/W2964641303","https://openalex.org/W2972147476"],"related_works":["https://openalex.org/W1973480752","https://openalex.org/W2805502594","https://openalex.org/W3132641048","https://openalex.org/W4253208712","https://openalex.org/W31439402","https://openalex.org/W2217679042","https://openalex.org/W1603677234","https://openalex.org/W2525971763","https://openalex.org/W2984753899","https://openalex.org/W2783178962"],"abstract_inverted_index":{"Structure-based":[0],"fragment":[1,31,99,167,224],"growing":[2,14],"is":[3,15,113,153],"one":[4],"of":[5,90,98,103,140,173,184,209,223],"the":[6,72,88,96,123,129,174,185,202,217],"key":[7],"techniques":[8],"in":[9,134],"fragment-based":[10],"drug":[11],"design.":[12],"Fragment":[13],"commonly":[16],"practiced":[17],"based":[18],"on":[19,115,127],"structural":[20],"and":[21,60,86,179],"biophysical":[22],"data.":[23],"Computational":[24],"workflows":[25,40],"are":[26,44,163],"employed":[27],"to":[28,35,46,57,71,75,149,165,171,182,201],"predict":[29],"which":[30],"elaborations":[32],"could":[33,191],"lead":[34],"high-affinity":[36],"binders.":[37],"Several":[38],"such":[39],"exist":[41],"but":[42],"many":[43],"designed":[45],"be":[47,58,69,159],"long":[48],"running":[49],"noninteractive":[50],"systems.":[51],"Shape-based":[52],"descriptors":[53,94,105],"have":[54],"been":[55],"proven":[56],"fast":[59,220],"perform":[61],"well":[62,145],"at":[63],"virtual-screening":[64],"tasks.":[65],"They":[66],"could,":[67],"therefore,":[68],"applied":[70],"fragment-growing":[73,79],"problem":[74],"enable":[76],"an":[77],"interactive":[78],"workflow.":[80],"In":[81],"this":[82],"work,":[83],"we":[84,107],"describe":[85],"analyze":[87],"use":[89],"specific":[91],"shape-based":[92],"directional":[93],"for":[95,180,219],"task":[97],"growing.":[100],"The":[101,138],"performance":[102,133],"these":[104],"that":[106,161],"call":[108],"ray":[109],"volume":[110],"matrices":[111],"(RVMs)":[112],"evaluated":[114],"two":[116],"data":[117],"sets":[118],"containing":[119],"protein-ligand":[120],"complexes.":[121],"While":[122],"first":[124],"set":[125],"focuses":[126],"self-growing,":[128],"second":[130],"measures":[131],"practical":[132],"a":[135],"cross-growing":[136,188],"scenario.":[137],"runtime":[139],"screenings":[141,222],"using":[142],"RVMs":[143,162,190],"as":[144,146],"their":[147],"robustness":[148],"three":[150],"dimensional":[151],"perturbations":[152],"also":[154],"investigated.":[155],"Overall,":[156],"it":[157],"can":[158],"shown":[160],"useful":[164],"prefilter":[166],"candidates.":[168],"For":[169],"up":[170,181],"84%":[172],"3299":[175],"generated":[176,187],"self-growing":[177],"cases":[178],"66%":[183],"326":[186],"cases,":[189],"create":[192],"poses":[193],"with":[194,205],"less":[195],"than":[196],"2":[197],"\u00c5":[198],"root-mean-square":[199],"deviation":[200],"crystal":[203],"structure":[204],"average":[206],"query":[207],"speeds":[208],"around":[210],"30,000":[211],"conformations":[212],"per":[213],"second.":[214],"This":[215],"opens":[216],"door":[218],"explorative":[221],"libraries.":[225]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3}],"updated_date":"2026-05-03T08:25:01.440150","created_date":"2025-10-10T00:00:00"}