{"id":"https://openalex.org/W1970799005","doi":"https://doi.org/10.1021/ci200454v","title":"Combining Global and Local Measures for Structure-Based Druggability Predictions","display_name":"Combining Global and Local Measures for Structure-Based Druggability Predictions","publication_year":2011,"publication_date":"2011-12-08","ids":{"openalex":"https://openalex.org/W1970799005","doi":"https://doi.org/10.1021/ci200454v","mag":"1970799005","pmid":"https://pubmed.ncbi.nlm.nih.gov/22148551"},"language":"en","primary_location":{"id":"doi:10.1021/ci200454v","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200454v","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/A5057416678","display_name":"Andrea Volkamer","orcid":"https://orcid.org/0000-0002-3760-580X"},"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":"Andrea Volkamer","raw_affiliation_strings":["University of Hamburg, Center\rfor Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany","University of Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"University of Hamburg, Center\rfor Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]},{"raw_affiliation_string":"University of Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078316788","display_name":"Daniel K\u00fchn","orcid":"https://orcid.org/0000-0002-0550-4174"},"institutions":[{"id":"https://openalex.org/I164928964","display_name":"Merck (Germany)","ror":"https://ror.org/04b2dty93","country_code":"DE","type":"company","lineage":["https://openalex.org/I164928964"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Daniel Kuhn","raw_affiliation_strings":["Merck KGaA, Merck Serono, Global\rComputational Chemistry, Frankfurter Str. 250, 64293 Darmstadt, Germany","Merck KGaA, Merck Serono, Global#R#Computational Chemistry, Frankfurter Str. 250, 64293 Darmstadt, Germany"],"affiliations":[{"raw_affiliation_string":"Merck KGaA, Merck Serono, Global\rComputational Chemistry, Frankfurter Str. 250, 64293 Darmstadt, Germany","institution_ids":["https://openalex.org/I164928964"]},{"raw_affiliation_string":"Merck KGaA, Merck Serono, Global#R#Computational Chemistry, Frankfurter Str. 250, 64293 Darmstadt, Germany","institution_ids":["https://openalex.org/I164928964"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002611995","display_name":"Thomas Grombacher","orcid":"https://orcid.org/0000-0001-9855-7429"},"institutions":[{"id":"https://openalex.org/I164928964","display_name":"Merck (Germany)","ror":"https://ror.org/04b2dty93","country_code":"DE","type":"company","lineage":["https://openalex.org/I164928964"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas Grombacher","raw_affiliation_strings":["Merck KGaA, Merck Serono, Bioinformatics,\rFrankfurter Str. 250, 64293 Darmstadt, Germany","Merck KGaA, Merck Serono, Bioinformatics,#R#Frankfurter Str. 250, 64293 Darmstadt, Germany"],"affiliations":[{"raw_affiliation_string":"Merck KGaA, Merck Serono, Bioinformatics,\rFrankfurter Str. 250, 64293 Darmstadt, Germany","institution_ids":["https://openalex.org/I164928964"]},{"raw_affiliation_string":"Merck KGaA, Merck Serono, Bioinformatics,#R#Frankfurter Str. 250, 64293 Darmstadt, Germany","institution_ids":["https://openalex.org/I164928964"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013173045","display_name":"Friedrich Rippmann","orcid":"https://orcid.org/0000-0002-4604-9251"},"institutions":[{"id":"https://openalex.org/I164928964","display_name":"Merck (Germany)","ror":"https://ror.org/04b2dty93","country_code":"DE","type":"company","lineage":["https://openalex.org/I164928964"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Friedrich Rippmann","raw_affiliation_strings":["Merck KGaA, Merck Serono, Global\rComputational Chemistry, Frankfurter Str. 250, 64293 Darmstadt, Germany","Merck KGaA, Merck Serono, Global#R#Computational Chemistry, Frankfurter Str. 250, 64293 Darmstadt, Germany"],"affiliations":[{"raw_affiliation_string":"Merck KGaA, Merck Serono, Global\rComputational Chemistry, Frankfurter Str. 250, 64293 Darmstadt, Germany","institution_ids":["https://openalex.org/I164928964"]},{"raw_affiliation_string":"Merck KGaA, Merck Serono, Global#R#Computational Chemistry, Frankfurter Str. 250, 64293 Darmstadt, Germany","institution_ids":["https://openalex.org/I164928964"]}]},{"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":false,"raw_author_name":"Matthias Rarey","raw_affiliation_strings":["University of Hamburg, Center\rfor Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany","University of Hamburg, Center#R#for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"University of Hamburg, Center\rfor Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]},{"raw_affiliation_string":"University of Hamburg, Center#R#for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5057416678"],"corresponding_institution_ids":["https://openalex.org/I159176309"],"apc_list":null,"apc_paid":null,"fwci":14.6488,"has_fulltext":false,"cited_by_count":484,"citation_normalized_percentile":{"value":0.99451035,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"52","issue":"2","first_page":"360","last_page":"372"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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":0.9779000282287598,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9503999948501587,"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/druggability","display_name":"Druggability","score":0.9883325099945068},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5914059281349182},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.5224020481109619},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4539473056793213},{"id":"https://openalex.org/keywords/k-nearest-neighbors-algorithm","display_name":"k-nearest neighbors algorithm","score":0.45162031054496765},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.445658415555954},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4440566599369049},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38988563418388367},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34077781438827515},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2916942238807678},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16405925154685974},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12507778406143188}],"concepts":[{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.9883325099945068},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5914059281349182},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.5224020481109619},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4539473056793213},{"id":"https://openalex.org/C113238511","wikidata":"https://www.wikidata.org/wiki/Q1071612","display_name":"k-nearest neighbors algorithm","level":2,"score":0.45162031054496765},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.445658415555954},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4440566599369049},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38988563418388367},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34077781438827515},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2916942238807678},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16405925154685974},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12507778406143188},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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":"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":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","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":"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":"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":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci200454v","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200454v","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:22148551","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22148551","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":"Reduced inequalities","score":0.6600000262260437,"id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W172019652","https://openalex.org/W1571577887","https://openalex.org/W1966496513","https://openalex.org/W1972844855","https://openalex.org/W1976142980","https://openalex.org/W1979598348","https://openalex.org/W1981064967","https://openalex.org/W1999391843","https://openalex.org/W1999711931","https://openalex.org/W2009737286","https://openalex.org/W2010750139","https://openalex.org/W2013600324","https://openalex.org/W2016240585","https://openalex.org/W2018408116","https://openalex.org/W2019951137","https://openalex.org/W2019971393","https://openalex.org/W2036884070","https://openalex.org/W2044703506","https://openalex.org/W2052314111","https://openalex.org/W2052643996","https://openalex.org/W2062187228","https://openalex.org/W2074370114","https://openalex.org/W2074978479","https://openalex.org/W2079953901","https://openalex.org/W2085491337","https://openalex.org/W2092285329","https://openalex.org/W2140407975","https://openalex.org/W2145465608","https://openalex.org/W2164088236","https://openalex.org/W2170146596","https://openalex.org/W3101467075"],"related_works":["https://openalex.org/W2556855892","https://openalex.org/W4280541024","https://openalex.org/W1969888071","https://openalex.org/W2035422779","https://openalex.org/W2925167008","https://openalex.org/W2036884070","https://openalex.org/W2008033400","https://openalex.org/W2903181389","https://openalex.org/W3023385275","https://openalex.org/W1972982874"],"abstract_inverted_index":{"Predicting":[0],"druggability":[1,30,65,168,213,247],"and":[2,29,61,69,84,120,161,175,184,204,221],"prioritizing":[3],"certain":[4],"disease":[5],"modifying":[6],"targets":[7,79],"for":[8,27,191,211],"the":[9,38,64,90,92,122,154,158,162,216,228],"drug":[10],"development":[11],"process":[12],"is":[13,22,178,240],"of":[14,34,37,54,77,89,135,153,218,231],"high":[15],"practical":[16],"relevance":[17],"in":[18,133],"pharmaceutical":[19],"research.":[20],"DoGSiteScorer":[21],"a":[23,55,101,136,244],"fully":[24],"automatic":[25,212,229],"algorithm":[26],"pocket":[28,123,128,156,193,209,219,238],"prediction.":[31,214,248],"Besides":[32],"consideration":[33],"global":[35,97,109,192,208],"properties":[36,110,129,239],"pocket,":[39],"also":[40],"local":[41,127,237],"similarities":[42,141],"shared":[43],"between":[44,148,173],"pockets":[45,177],"are":[46,50,130,142,206],"reflected.":[47],"Druggability":[48],"scores":[49],"predicted":[51],"by":[52,144],"means":[53],"support":[56],"vector":[57],"machine":[58],"(SVM),":[59],"trained,":[60],"tested":[62],"on":[63,96],"data":[66],"set":[67],"(DD)":[68],"its":[70],"nonredundant":[71],"version":[72],"(NRDD).":[73],"The":[74],"DD":[75,155],"consists":[76],"1069":[78],"with":[80,166,196],"assigned":[81],"druggable,":[82],"difficult,":[83],"undruggable":[85,176],"classes.":[86],"In":[87,151],"90%":[88],"NRDD,":[91],"SVM":[93],"model":[94],"based":[95],"descriptors":[98,194,210],"correctly":[99],"classifies":[100],"target":[102],"as":[103],"either":[104],"druggable":[105,174,232],"or":[106],"undruggable.":[107],"Nevertheless,":[108,215],"suffer":[111],"from":[112,121],"binding":[113,119,226],"site":[114],"changes":[115],"due":[116],"to":[117],"ligand":[118,225],"boundary":[124],"definition.":[125],"Therefore,":[126],"additionally":[131],"investigated":[132],"terms":[134],"nearest":[137,159],"neighbor":[138,160],"search.":[139],"Local":[140],"described":[143],"distance":[145],"dependent":[146],"histograms":[147],"atom":[149],"pairs.":[150,188],"88%":[152],"set,":[157],"structure":[163],"itself":[164],"conform":[165],"their":[167,222],"type.":[169],"A":[170],"discriminant":[171],"feature":[172],"having":[179],"less":[180],"short-range":[181,186],"hydrophilic-hydrophilic":[182],"pairs":[183],"more":[185],"lipophilic-lipophilic":[187],"Our":[189],"findings":[190],"coincide":[195],"previously":[197],"published":[198],"methods":[199],"affirming":[200],"that":[201],"size,":[202],"shape,":[203],"hydrophobicity":[205],"important":[207],"variety":[217],"shapes":[220],"flexibility":[223],"upon":[224],"limit":[227],"projection":[230],"features":[233],"onto":[234],"descriptors.":[235],"Incorporating":[236],"another":[241],"step":[242],"toward":[243],"reliable":[245],"descriptor-based":[246]},"counts_by_year":[{"year":2026,"cited_by_count":16},{"year":2025,"cited_by_count":53},{"year":2024,"cited_by_count":48},{"year":2023,"cited_by_count":46},{"year":2022,"cited_by_count":62},{"year":2021,"cited_by_count":50},{"year":2020,"cited_by_count":45},{"year":2019,"cited_by_count":26},{"year":2018,"cited_by_count":19},{"year":2017,"cited_by_count":26},{"year":2016,"cited_by_count":24},{"year":2015,"cited_by_count":24},{"year":2014,"cited_by_count":22},{"year":2013,"cited_by_count":14},{"year":2012,"cited_by_count":8}],"updated_date":"2026-03-24T08:02:53.985720","created_date":"2025-10-10T00:00:00"}