{"id":"https://openalex.org/W2027974277","doi":"https://doi.org/10.1021/ci4000163","title":"In Silico Fragment-Based Drug Discovery: Setup and Validation of a Fragment-to-Lead Computational Protocol Using S4MPLE","display_name":"In Silico Fragment-Based Drug Discovery: Setup and Validation of a Fragment-to-Lead Computational Protocol Using S4MPLE","publication_year":2013,"publication_date":"2013-03-28","ids":{"openalex":"https://openalex.org/W2027974277","doi":"https://doi.org/10.1021/ci4000163","mag":"2027974277","pmid":"https://pubmed.ncbi.nlm.nih.gov/23537132"},"language":"en","primary_location":{"id":"doi:10.1021/ci4000163","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci4000163","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/A5105510950","display_name":"Laurent Hoffer","orcid":"https://orcid.org/0000-0003-1906-7128"},"institutions":[{"id":"https://openalex.org/I68947357","display_name":"Universit\u00e9 de Strasbourg","ror":"https://ror.org/00pg6eq24","country_code":"FR","type":"education","lineage":["https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Laurent Hoffer","raw_affiliation_strings":["NovAliX, BioParc, bld S\u00e9bastien\rBrant, BP 30170, Illkirch 67405 Cedex, France","Universit\u00e9 de Strasbourg,\r1 rue B. Pascal, Strasbourg 67000, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NovAliX, BioParc, bld S\u00e9bastien\rBrant, BP 30170, Illkirch 67405 Cedex, France","institution_ids":[]},{"raw_affiliation_string":"Universit\u00e9 de Strasbourg,\r1 rue B. Pascal, Strasbourg 67000, France","institution_ids":["https://openalex.org/I68947357"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044186954","display_name":"Jean\u2010Paul Renaud","orcid":"https://orcid.org/0000-0001-9180-5426"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jean-Paul Renaud","raw_affiliation_strings":["NovAliX, BioParc, bld S\u00e9bastien\rBrant, BP 30170, Illkirch 67405 Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NovAliX, BioParc, bld S\u00e9bastien\rBrant, BP 30170, Illkirch 67405 Cedex, France","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031667486","display_name":"Dragos Horvath","orcid":"https://orcid.org/0000-0003-0173-5714"},"institutions":[{"id":"https://openalex.org/I68947357","display_name":"Universit\u00e9 de Strasbourg","ror":"https://ror.org/00pg6eq24","country_code":"FR","type":"education","lineage":["https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Dragos Horvath","raw_affiliation_strings":["Universit\u00e9 de Strasbourg,\r1 rue B. Pascal, Strasbourg 67000, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 de Strasbourg,\r1 rue B. Pascal, Strasbourg 67000, France","institution_ids":["https://openalex.org/I68947357"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5031667486"],"corresponding_institution_ids":["https://openalex.org/I68947357"],"apc_list":null,"apc_paid":null,"fwci":2.9162,"has_fulltext":false,"cited_by_count":37,"citation_normalized_percentile":{"value":0.90657959,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"53","issue":"4","first_page":"836","last_page":"851"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9919999837875366,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.983299970626831,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.7736132740974426},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.7406631708145142},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.6247416734695435},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5974760055541992},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5972512364387512},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5489358305931091},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4625593423843384},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.45310255885124207},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.419800341129303},{"id":"https://openalex.org/keywords/dock","display_name":"DOCK","score":0.41781097650527954},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.41273701190948486},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19199568033218384},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14310264587402344},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.12885695695877075},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09935438632965088}],"concepts":[{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.7736132740974426},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.7406631708145142},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6247416734695435},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5974760055541992},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5972512364387512},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5489358305931091},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4625593423843384},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.45310255885124207},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.419800341129303},{"id":"https://openalex.org/C93073132","wikidata":"https://www.wikidata.org/wiki/Q24726581","display_name":"DOCK","level":2,"score":0.41781097650527954},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.41273701190948486},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19199568033218384},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14310264587402344},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.12885695695877075},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09935438632965088},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"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":"D000095","descriptor_name":"Acetolactate Synthase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000095","descriptor_name":"Acetolactate Synthase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000095","descriptor_name":"Acetolactate Synthase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","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":false},{"descriptor_ui":"D015951","descriptor_name":"Factor Xa","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015951","descriptor_name":"Factor Xa","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015951","descriptor_name":"Factor Xa","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018841","descriptor_name":"HSP90 Heat-Shock Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018841","descriptor_name":"HSP90 Heat-Shock Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018841","descriptor_name":"HSP90 Heat-Shock Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","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":2,"locations":[{"id":"doi:10.1021/ci4000163","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci4000163","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:23537132","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23537132","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":[{"display_name":"Clean water and sanitation","id":"https://metadata.un.org/sdg/6","score":0.47999998927116394}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322147","display_name":"Universit\u00e9 de Strasbourg","ror":"https://ror.org/00pg6eq24"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":78,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1509196567","https://openalex.org/W1518367201","https://openalex.org/W1592238003","https://openalex.org/W1919867164","https://openalex.org/W1963607000","https://openalex.org/W1964183799","https://openalex.org/W1967368966","https://openalex.org/W1969909141","https://openalex.org/W1972091733","https://openalex.org/W1974086930","https://openalex.org/W1981429394","https://openalex.org/W1983194490","https://openalex.org/W1985588649","https://openalex.org/W1988598882","https://openalex.org/W1991286793","https://openalex.org/W1996100382","https://openalex.org/W1997469763","https://openalex.org/W2001054421","https://openalex.org/W2006720282","https://openalex.org/W2008525757","https://openalex.org/W2009299989","https://openalex.org/W2011230643","https://openalex.org/W2011391967","https://openalex.org/W2011736771","https://openalex.org/W2014091120","https://openalex.org/W2015688756","https://openalex.org/W2016393702","https://openalex.org/W2022476850","https://openalex.org/W2022749059","https://openalex.org/W2023251219","https://openalex.org/W2024705685","https://openalex.org/W2027087190","https://openalex.org/W2031609935","https://openalex.org/W2032924120","https://openalex.org/W2034475831","https://openalex.org/W2037825667","https://openalex.org/W2040154749","https://openalex.org/W2040948463","https://openalex.org/W2041686943","https://openalex.org/W2046813714","https://openalex.org/W2047710091","https://openalex.org/W2047819524","https://openalex.org/W2048245505","https://openalex.org/W2052933929","https://openalex.org/W2053010171","https://openalex.org/W2055704927","https://openalex.org/W2060531713","https://openalex.org/W2063523570","https://openalex.org/W2064265071","https://openalex.org/W2064514012","https://openalex.org/W2072359587","https://openalex.org/W2072544747","https://openalex.org/W2074978477","https://openalex.org/W2076419401","https://openalex.org/W2079391392","https://openalex.org/W2080618096","https://openalex.org/W2080653934","https://openalex.org/W2080914508","https://openalex.org/W2082474121","https://openalex.org/W2089248273","https://openalex.org/W2093381148","https://openalex.org/W2110845358","https://openalex.org/W2113863960","https://openalex.org/W2116211618","https://openalex.org/W2117996566","https://openalex.org/W2134486592","https://openalex.org/W2135732933","https://openalex.org/W2139827114","https://openalex.org/W2141715793","https://openalex.org/W2146984355","https://openalex.org/W2147993766","https://openalex.org/W2152477689","https://openalex.org/W2152491970","https://openalex.org/W2159701165","https://openalex.org/W2166704869","https://openalex.org/W2168045053","https://openalex.org/W2176516200"],"related_works":["https://openalex.org/W4282913408","https://openalex.org/W1980425862","https://openalex.org/W2100436540","https://openalex.org/W2300502530","https://openalex.org/W3201417569","https://openalex.org/W3033824302","https://openalex.org/W2070163817","https://openalex.org/W2091429460","https://openalex.org/W2102475066","https://openalex.org/W2395175315"],"abstract_inverted_index":{"This":[0,289],"paper":[1,54],"describes":[2],"the":[3,52,61,117,163,166,178,182,208,223,233,242,246,249,285,297,310],"use":[4],"and":[5,129,154,281,323,346],"validation":[6],"of":[7,51,64,87,91,116,207,245,264,284,318,326,330,351],"S4MPLE":[8,25,67,145,196,236],"in":[9,77],"Fragment-Based":[10],"Drug":[11],"Design":[12],"(FBDD)--a":[13],"strategy":[14,193,290],"to":[15,40,56,60,98,107,122,165,177,187,202,232,240,293,308],"build":[16,188],"drug-like":[17],"ligands":[18],"starting":[19,234],"from":[20,132,257,296],"small":[21],"compounds":[22],"called":[23],"fragments.":[24,235],"is":[26,38,55,104,237,272],"a":[27,33,101,189,204,214,219],"conformational":[28,344],"sampling":[29],"tool":[30],"based":[31,194,274],"on":[32,195,255,275],"hybrid":[34],"genetic":[35,65],"algorithm":[36],"that":[37,58,103],"able":[39],"simulate":[41],"one":[42,88],"(conformer":[43],"enumeration)":[44],"or":[45,89],"more":[46,338],"molecules":[47,173],"(docking).":[48],"The":[49,95,211],"goal":[50],"current":[53],"show":[57],"due":[59],"judicious":[62],"design":[63],"operators,":[66],"may":[68,138,146],"be":[69],"used":[70,239],"without":[71],"any":[72],"specific":[73],"adaptation":[74],"as":[75],"an":[76,262],"silico":[78],"FBDD":[79,298],"tool.":[80],"Such":[81],"fragment-to-lead":[82],"evolution":[83],"involves":[84],"either":[85],"growing":[86],"linking":[90],"several":[92,294,304],"fragment-like":[93],"binder(s).":[94],"native":[96],"ability":[97,307],"specifically":[99],"\"dock\"":[100],"substructure":[102],"covalently":[105],"anchored":[106],"its":[108],"target":[109],"(here,":[110],"some":[111],"prepositioned":[112],"fragment":[113,287],"formally":[114],"part":[115],"binding":[118,250,328,342],"site)":[119],"enables":[120],"it":[121,131,155],"act":[123],"like":[124],"dedicated":[125],"de":[126],"novo":[127],"builders":[128],"differentiates":[130],"most":[133],"classical":[134],"docking":[135],"tools,":[136],"which":[137],"only":[139,183],"cope":[140],"with":[141,252,300,348],"non-covalent":[142],"interactions.":[143,355],"Besides,":[144],"address":[147],"growing/linking":[148,192],"scenarios":[149],"involving":[150,341],"protein":[151],"site":[152,167,343],"flexibility,":[153],"might":[156],"also":[157],"suggest":[158],"\"growth\"":[159],"moves":[160],"by":[161,217,261],"bridging":[162],"ligand":[164,312],"via":[168],"water-mediated":[169,354],"interactions":[170],"if":[171],"H2O":[172],"are":[174],"simply":[175],"appended":[176],"input":[179],"files.":[180],"Therefore,":[181],"development":[184],"overhead":[185],"required":[186],"virtual":[190],"fragment\u2192ligand":[191],"were":[197],"two":[198,276],"chemoinformatics":[199],"programs":[200],"meant":[201],"provide":[203],"minimalistic":[205],"management":[206],"linker":[209],"library.":[210],"first":[212],"creates":[213],"duplicate-free":[215],"library":[216],"fragmenting":[218],"compound":[220],"database,":[221],"whereas":[222],"second":[224],"builds":[225],"new":[226],"compounds,":[227,322],"attaching":[228],"chemically":[229],"compatible":[230],"linkers":[231,247],"subsequently":[238],"probe":[241],"optimal":[243],"placement":[244],"within":[248],"site,":[251],"initial":[253,258],"restraints":[254],"atoms":[256],"fragments,":[259],"followed":[260],"optimization":[263],"all":[265],"kept":[266],"poses":[267],"after":[268],"restraint":[269],"removal.":[270],"Ranking":[271],"mainly":[273],"criteria:":[277,306],"force-field":[278],"potential":[279],"energy":[280],"RMSD":[282],"shifts":[283],"original":[286],"moieties.":[288],"was":[291],"applied":[292],"examples":[295],"literature":[299],"good":[301,316],"results":[302],"over":[303],"monitored":[305],"generate":[309],"optimized":[311],"(or":[313],"close":[314],"analogs),":[315],"ranking":[317],"analogs":[319],"among":[320],"decoy":[321],"accurate":[324],"predictions":[325],"expected":[327],"modes":[329],"reference":[331],"ligands.":[332],"Simulations":[333],"included":[334],"\"classical\"":[335],"covalent":[336],"growing/linking,":[337],"challenging":[339],"ones":[340],"changes,":[345],"growth":[347],"optional":[349],"recognition":[350],"putatively":[352],"favorable":[353]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}