{"id":"https://openalex.org/W2035162463","doi":"https://doi.org/10.1021/ci4001019","title":"Scaffold Hopping by Fragment Replacement","display_name":"Scaffold Hopping by Fragment Replacement","publication_year":2013,"publication_date":"2013-07-04","ids":{"openalex":"https://openalex.org/W2035162463","doi":"https://doi.org/10.1021/ci4001019","mag":"2035162463","pmid":"https://pubmed.ncbi.nlm.nih.gov/23826858"},"language":"en","primary_location":{"id":"doi:10.1021/ci4001019","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci4001019","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/A5084821408","display_name":"Mikko J. Vainio","orcid":"https://orcid.org/0000-0001-9005-6590"},"institutions":[{"id":"https://openalex.org/I4210143795","display_name":"AstraZeneca (Sweden)","ror":"https://ror.org/04wwrrg31","country_code":"SE","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210143795"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Mikko J. Vainio","raw_affiliation_strings":["Discovery Sciences Chemistry Innovation Centre, AstraZeneca R&D, Pepparedsleden 1, 43186 M\u00f6lndal, Sweden"],"affiliations":[{"raw_affiliation_string":"Discovery Sciences Chemistry Innovation Centre, AstraZeneca R&D, Pepparedsleden 1, 43186 M\u00f6lndal, Sweden","institution_ids":["https://openalex.org/I4210143795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031504624","display_name":"Thierry Kogej","orcid":null},"institutions":[{"id":"https://openalex.org/I4210143795","display_name":"AstraZeneca (Sweden)","ror":"https://ror.org/04wwrrg31","country_code":"SE","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210143795"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Thierry Kogej","raw_affiliation_strings":["Discovery Sciences Chemistry Innovation Centre, AstraZeneca R&D, Pepparedsleden 1, 43186 M\u00f6lndal, Sweden"],"affiliations":[{"raw_affiliation_string":"Discovery Sciences Chemistry Innovation Centre, AstraZeneca R&D, Pepparedsleden 1, 43186 M\u00f6lndal, Sweden","institution_ids":["https://openalex.org/I4210143795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039564402","display_name":"Florian Raubacher","orcid":null},"institutions":[{"id":"https://openalex.org/I4210143795","display_name":"AstraZeneca (Sweden)","ror":"https://ror.org/04wwrrg31","country_code":"SE","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210143795"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Florian Raubacher","raw_affiliation_strings":["Discovery Sciences Chemistry Innovation Centre, AstraZeneca R&D, Pepparedsleden 1, 43186 M\u00f6lndal, Sweden"],"affiliations":[{"raw_affiliation_string":"Discovery Sciences Chemistry Innovation Centre, AstraZeneca R&D, Pepparedsleden 1, 43186 M\u00f6lndal, Sweden","institution_ids":["https://openalex.org/I4210143795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010925151","display_name":"Jens Sadowski","orcid":"https://orcid.org/0000-0003-3507-1047"},"institutions":[{"id":"https://openalex.org/I4210143795","display_name":"AstraZeneca (Sweden)","ror":"https://ror.org/04wwrrg31","country_code":"SE","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210143795"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Jens Sadowski","raw_affiliation_strings":["Discovery Sciences Chemistry Innovation Centre, AstraZeneca R&D, Pepparedsleden 1, 43186 M\u00f6lndal, Sweden"],"affiliations":[{"raw_affiliation_string":"Discovery Sciences Chemistry Innovation Centre, AstraZeneca R&D, Pepparedsleden 1, 43186 M\u00f6lndal, Sweden","institution_ids":["https://openalex.org/I4210143795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5084821408"],"corresponding_institution_ids":["https://openalex.org/I4210143795"],"apc_list":null,"apc_paid":null,"fwci":4.1025,"has_fulltext":false,"cited_by_count":44,"citation_normalized_percentile":{"value":0.93921011,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"53","issue":"7","first_page":"1825","last_page":"1835"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994999766349792,"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":0.9994999766349792,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9962999820709229,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9778000116348267,"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/scaffold","display_name":"Scaffold","score":0.8289478421211243},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7039204835891724},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.6369130611419678},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6025013327598572},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5525962710380554},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.5302666425704956},{"id":"https://openalex.org/keywords/frame","display_name":"Frame (networking)","score":0.49391037225723267},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4548041522502899},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4194909632205963},{"id":"https://openalex.org/keywords/orientation","display_name":"Orientation (vector space)","score":0.41458219289779663},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3293517231941223},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.24091479182243347},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19606760144233704},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15970656275749207},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.10473978519439697},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09475663304328918},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.07757845520973206}],"concepts":[{"id":"https://openalex.org/C89429830","wikidata":"https://www.wikidata.org/wiki/Q735710","display_name":"Scaffold","level":2,"score":0.8289478421211243},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7039204835891724},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.6369130611419678},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6025013327598572},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5525962710380554},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.5302666425704956},{"id":"https://openalex.org/C126042441","wikidata":"https://www.wikidata.org/wiki/Q1324888","display_name":"Frame (networking)","level":2,"score":0.49391037225723267},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4548041522502899},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4194909632205963},{"id":"https://openalex.org/C16345878","wikidata":"https://www.wikidata.org/wiki/Q107472979","display_name":"Orientation (vector space)","level":2,"score":0.41458219289779663},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3293517231941223},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.24091479182243347},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19606760144233704},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15970656275749207},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.10473978519439697},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09475663304328918},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.07757845520973206},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005240","descriptor_name":"Feasibility Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005240","descriptor_name":"Feasibility Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005240","descriptor_name":"Feasibility Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"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":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},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci4001019","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci4001019","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:23826858","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23826858","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":[{"id":"https://metadata.un.org/sdg/3","score":0.6499999761581421,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1604884792","https://openalex.org/W1968299916","https://openalex.org/W1975147762","https://openalex.org/W1988037271","https://openalex.org/W1991286793","https://openalex.org/W1997575697","https://openalex.org/W2005465759","https://openalex.org/W2009660063","https://openalex.org/W2014540789","https://openalex.org/W2015907087","https://openalex.org/W2018621056","https://openalex.org/W2022395659","https://openalex.org/W2025829414","https://openalex.org/W2028015629","https://openalex.org/W2028232877","https://openalex.org/W2029665189","https://openalex.org/W2033293438","https://openalex.org/W2035349592","https://openalex.org/W2042110087","https://openalex.org/W2042212296","https://openalex.org/W2050081695","https://openalex.org/W2057350662","https://openalex.org/W2058820833","https://openalex.org/W2067300585","https://openalex.org/W2070332197","https://openalex.org/W2075186867","https://openalex.org/W2075894968","https://openalex.org/W2076018790","https://openalex.org/W2077703786","https://openalex.org/W2078374001","https://openalex.org/W2079991727","https://openalex.org/W2089248273","https://openalex.org/W2093814531","https://openalex.org/W2094120651","https://openalex.org/W2096541451","https://openalex.org/W2100260986","https://openalex.org/W2108245251","https://openalex.org/W2122576346","https://openalex.org/W2132802776","https://openalex.org/W2138188160","https://openalex.org/W2141303613","https://openalex.org/W2147421370","https://openalex.org/W2160592148","https://openalex.org/W2165843192","https://openalex.org/W2170164763","https://openalex.org/W2477052610","https://openalex.org/W4230274588"],"related_works":["https://openalex.org/W1973480752","https://openalex.org/W2805502594","https://openalex.org/W4253208712","https://openalex.org/W1603677234","https://openalex.org/W3132641048","https://openalex.org/W2217679042","https://openalex.org/W2525971763","https://openalex.org/W2984753899","https://openalex.org/W2783178962","https://openalex.org/W1896179566"],"abstract_inverted_index":{"This":[0],"work":[1,82],"describes":[2],"a":[3,27,84,109,141,147],"data":[4],"driven":[5],"method":[6],"for":[7,88,95,106,140],"scaffold":[8,99],"hopping":[9],"by":[10,20],"fragment":[11],"replacement.":[12],"A":[13,67,98],"search":[14],"database":[15],"of":[16,23,32,46,143],"scaffolds":[17,34,57,139],"is":[18,102,132],"created":[19],"cutting":[21],"bonds":[22,49],"existing":[24],"compounds":[25],"in":[26,74,146,158],"combinatorial":[28],"fashion.":[29],"Three-dimensional":[30],"structures":[31],"the":[33,43,47,75,89,116,120,123,152],"are":[35,58],"then":[36],"generated":[37],"and":[38,63,78,114,122],"made":[39],"searchable":[40],"based":[41],"on":[42],"relative":[44],"orientation":[45],"broken":[48],"using":[50,60],"an":[51],"auxiliary":[52],"index":[53],"file.":[54],"The":[55,80,127],"retrieved":[56],"ranked":[59],"volume":[61],"overlap":[62],"electrostatic":[64],"similarity":[65,118],"scores.":[66],"similar":[68],"approach":[69],"has":[70],"been":[71],"used":[72,157],"before":[73],"program":[76,153],"CAVEAT":[77],"others.":[79],"present":[81],"introduces":[83],"novel":[85],"indexing":[86],"scheme":[87],"attachment":[90,111],"vector":[91,112],"geometry,":[92],"which":[93,104],"allows":[94,105],"fast":[96],"searching.":[97],"shape":[100,117],"descriptor":[101],"defined,":[103],"queries":[107,145],"with":[108],"single":[110],"(R-groups)":[113],"improves":[115],"between":[119],"query":[121],"suggested":[124],"replacement":[125,138],"fragments.":[126],"program,":[128],"called":[129],"Scaffold":[130],"Hopping,":[131],"shown":[133],"to":[134,155],"retrieve":[135],"relevant":[136],"bioisosteric":[137],"set":[142],"example":[144],"reasonable":[148],"time":[149],"frame,":[150],"making":[151],"suitable":[154],"be":[156],"drug":[159],"design":[160],"work.":[161]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2}],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}
