{"id":"https://openalex.org/W2887346809","doi":"https://doi.org/10.1021/acs.jcim.8b00385","title":"Exploring Activity Profiles of PAINS and Their Structural Context in Target\u2013Ligand Complexes","display_name":"Exploring Activity Profiles of PAINS and Their Structural Context in Target\u2013Ligand Complexes","publication_year":2018,"publication_date":"2018-08-14","ids":{"openalex":"https://openalex.org/W2887346809","doi":"https://doi.org/10.1021/acs.jcim.8b00385","mag":"2887346809","pmid":"https://pubmed.ncbi.nlm.nih.gov/30105913"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.8b00385","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00385","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/A5042866883","display_name":"Vishal B. Siramshetty","orcid":"https://orcid.org/0000-0002-5980-8288"},"institutions":[{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"funder","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Vishal B. Siramshetty","raw_affiliation_strings":["BB3R - Berlin Brandenburg 3R Graduate School, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany","Structural Bioinformatics Group, Charit\u00e9-Universit\u00e4tsmedizin Berlin, 10115 Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"BB3R - Berlin Brandenburg 3R Graduate School, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany","institution_ids":["https://openalex.org/I75951250"]},{"raw_affiliation_string":"Structural Bioinformatics Group, Charit\u00e9-Universit\u00e4tsmedizin Berlin, 10115 Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043414157","display_name":"Robert Prei\u00dfner","orcid":"https://orcid.org/0000-0002-2407-1087"},"institutions":[{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"funder","lineage":["https://openalex.org/I7877124"]},{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Robert Preissner","raw_affiliation_strings":["BB3R - Berlin Brandenburg 3R Graduate School, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany","Structural Bioinformatics Group, Charit\u00e9-Universit\u00e4tsmedizin Berlin, 10115 Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"BB3R - Berlin Brandenburg 3R Graduate School, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany","institution_ids":["https://openalex.org/I75951250"]},{"raw_affiliation_string":"Structural Bioinformatics Group, Charit\u00e9-Universit\u00e4tsmedizin Berlin, 10115 Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060130832","display_name":"Bj\u00f6rn-Oliver Gohlke","orcid":"https://orcid.org/0000-0003-3094-1031"},"institutions":[{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"funder","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Bjoern-Oliver Gohlke","raw_affiliation_strings":["Structural Bioinformatics Group, Charit\u00e9-Universit\u00e4tsmedizin Berlin, 10115 Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Structural Bioinformatics Group, Charit\u00e9-Universit\u00e4tsmedizin Berlin, 10115 Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5060130832"],"corresponding_institution_ids":["https://openalex.org/I7877124"],"apc_list":null,"apc_paid":null,"fwci":1.6155,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.85693256,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"58","issue":"9","first_page":"1847","last_page":"1857"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9854000210762024,"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":0.9711999893188477,"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/context","display_name":"Context (archaeology)","score":0.7564306259155273},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.526216983795166},{"id":"https://openalex.org/keywords/extrapolation","display_name":"Extrapolation","score":0.5033623576164246},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.4970252811908722},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4720041751861572},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4367111921310425},{"id":"https://openalex.org/keywords/ligand-efficiency","display_name":"Ligand efficiency","score":0.4298692047595978},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39056187868118286},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38538438081741333},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3523077666759491},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.3394054174423218},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21856316924095154},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1665745973587036},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15324869751930237},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.13160783052444458}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.7564306259155273},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.526216983795166},{"id":"https://openalex.org/C132459708","wikidata":"https://www.wikidata.org/wiki/Q744069","display_name":"Extrapolation","level":2,"score":0.5033623576164246},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.4970252811908722},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4720041751861572},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4367111921310425},{"id":"https://openalex.org/C204171352","wikidata":"https://www.wikidata.org/wiki/Q6545861","display_name":"Ligand efficiency","level":4,"score":0.4298692047595978},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39056187868118286},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38538438081741333},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3523077666759491},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3394054174423218},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21856316924095154},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1665745973587036},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15324869751930237},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.13160783052444458},{"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/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"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":"D001681","descriptor_name":"Biological Assay","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001681","descriptor_name":"Biological Assay","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001681","descriptor_name":"Biological Assay","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","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":true},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.8b00385","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00385","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:30105913","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30105913","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":[{"id":"https://openalex.org/G7349063869","display_name":null,"funder_award_id":"031A262C","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W1182581869","https://openalex.org/W1752612204","https://openalex.org/W1969293071","https://openalex.org/W1971963414","https://openalex.org/W1972821149","https://openalex.org/W1974003892","https://openalex.org/W1975875968","https://openalex.org/W1979600197","https://openalex.org/W1985176332","https://openalex.org/W1988765421","https://openalex.org/W1992243758","https://openalex.org/W1996295408","https://openalex.org/W1997349336","https://openalex.org/W1999676874","https://openalex.org/W2010401625","https://openalex.org/W2016969958","https://openalex.org/W2019883194","https://openalex.org/W2024908724","https://openalex.org/W2026509352","https://openalex.org/W2029582225","https://openalex.org/W2031441006","https://openalex.org/W2036922942","https://openalex.org/W2043509228","https://openalex.org/W2045722951","https://openalex.org/W2046337039","https://openalex.org/W2055475531","https://openalex.org/W2060341378","https://openalex.org/W2060581674","https://openalex.org/W2071737415","https://openalex.org/W2085590224","https://openalex.org/W2089966673","https://openalex.org/W2096560421","https://openalex.org/W2097559461","https://openalex.org/W2125782931","https://openalex.org/W2127287358","https://openalex.org/W2130479394","https://openalex.org/W2137676811","https://openalex.org/W2145803535","https://openalex.org/W2147670638","https://openalex.org/W2159266419","https://openalex.org/W2203407462","https://openalex.org/W2222431004","https://openalex.org/W2271027226","https://openalex.org/W2327974216","https://openalex.org/W2337652751","https://openalex.org/W2474575800","https://openalex.org/W2519670684","https://openalex.org/W2550870820","https://openalex.org/W2586253560","https://openalex.org/W2594683834","https://openalex.org/W2602196942","https://openalex.org/W2606217927","https://openalex.org/W2735467165","https://openalex.org/W2735853102","https://openalex.org/W2757556159","https://openalex.org/W2765398514","https://openalex.org/W2774836366","https://openalex.org/W2781998485","https://openalex.org/W2783556635","https://openalex.org/W2790459822","https://openalex.org/W2795039795"],"related_works":["https://openalex.org/W2023507136","https://openalex.org/W2024868635","https://openalex.org/W2137370364","https://openalex.org/W3008230527","https://openalex.org/W1417552894","https://openalex.org/W34989162","https://openalex.org/W2324976525","https://openalex.org/W1427625625","https://openalex.org/W3176501738","https://openalex.org/W4244376581"],"abstract_inverted_index":{"Assay":[0],"interference":[1,11],"is":[2,80,209,229],"an":[3],"acknowledged":[4],"problem":[5],"in":[6,164,180],"high-throughput":[7],"screening,":[8],"and":[9,50,65,92,99,105,125,146,151,225],"pan-assay":[10],"compounds":[12,114],"(PAINS)":[13],"filters":[14,214,228],"are":[15,96],"one":[16],"of":[17,20,28,43,61,69,76,108,157,173,189,222,236,242],"a":[18,73,220],"number":[19],"approaches":[21],"that":[22,39,183,206],"have":[23,37],"been":[24],"suggested":[25],"for":[26,187,199],"identification":[27],"potential":[29],"screening":[30,238],"artifacts":[31],"or":[32],"frequent":[33],"hitters.":[34],"Many":[35,177],"studies":[36],"highlighted":[38],"the":[40,55,62,66,93,102,133,147,158,160,170,174,190,233,243],"unwary":[41],"usage":[42],"these":[44],"structural":[45,67],"alerts":[46],"should":[47],"be":[48],"reconsidered":[49],"criticized":[51],"their":[52,194],"extrapolation":[53,79],"beyond":[54],"applicability":[56],"domain.":[57],"A":[58],"large-scale":[59],"investigation":[60],"activity":[63,106],"profiles":[64,107],"context":[68],"PAINS":[70,94,109,118,121,143,161,178,227],"might":[71],"provide":[72],"better":[74],"assessment":[75],"whether":[77],"this":[78,83],"valid.":[81],"To":[82],"end,":[84],"multiple":[85],"publicly":[86],"accessible":[87],"compound":[88,213],"collections":[89],"were":[90,110,144,149,184],"screened,":[91],"statistics":[95],"comprehensively":[97],"presented":[98],"discussed.":[100],"Next,":[101],"promiscuity":[103,124],"trends":[104],"compared":[111,131,168],"with":[112,132,169],"those":[113,197],"not":[115],"matching":[116,240],"any":[117,241],"substructures.":[119],"Overall,":[120],"demonstrated":[122],"higher":[123,127],"relatively":[126],"assay":[128,200],"hit":[129],"rates":[130],"other":[134],"compounds.":[135],"Furthermore,":[136],"nearly":[137],"2000":[138],"distinct":[139],"target-ligand":[140],"complexes":[141],"containing":[142],"analyzed,":[145],"interactions":[148,165,182],"quantified":[150],"compared.":[152],"In":[153,202],"more":[154,166],"than":[155],"50%":[156],"instances,":[159],"atoms":[162,172],"participated":[163,179],"frequently":[167],"remaining":[171],"ligand":[175],"structure.":[176],"crucial":[181],"often":[185],"responsible":[186,198],"binding":[188],"ligand,":[191],"which":[192],"reaffirms":[193],"distinction":[195],"from":[196],"interference.":[201],"conclusion,":[203],"we":[204],"reinforce":[205],"while":[207],"it":[208],"important":[210],"to":[211,215,231],"employ":[212],"eliminate":[216],"nonspecific":[217],"hits,":[218],"establishing":[219],"set":[221],"statistically":[223],"significant":[224],"validated":[226],"essential":[230],"restrain":[232],"black-box":[234],"practice":[235],"triaging":[237],"hits":[239],"proposed":[244],"480":[245],"alerts.":[246]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
