{"id":"https://openalex.org/W2024502043","doi":"https://doi.org/10.1186/1758-2946-2-s1-p42","title":"Automatic pharmacophore model generation using weighted substructure assignments","display_name":"Automatic pharmacophore model generation using weighted substructure assignments","publication_year":2010,"publication_date":"2010-05-01","ids":{"openalex":"https://openalex.org/W2024502043","doi":"https://doi.org/10.1186/1758-2946-2-s1-p42","mag":"2024502043"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-2-s1-p42","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-p42","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P42","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P42","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066354297","display_name":"Andreas Jahn","orcid":"https://orcid.org/0000-0003-0207-0224"},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Andreas Jahn","raw_affiliation_strings":["University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","University of T\u00fcbingen, T\u00fcbingen, Germany#TAB#"],"affiliations":[{"raw_affiliation_string":"University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"University of T\u00fcbingen, T\u00fcbingen, Germany#TAB#","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004102781","display_name":"Hannes Planatscher","orcid":"https://orcid.org/0000-0002-6536-0782"},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"H Planatscher","raw_affiliation_strings":["University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","University of T\u00fcbingen, T\u00fcbingen, Germany#TAB#"],"affiliations":[{"raw_affiliation_string":"University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"University of T\u00fcbingen, T\u00fcbingen, Germany#TAB#","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035710038","display_name":"Georg Hinselmann","orcid":null},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Georg Hinselmann","raw_affiliation_strings":["University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","University of T\u00fcbingen, T\u00fcbingen, Germany#TAB#"],"affiliations":[{"raw_affiliation_string":"University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"University of T\u00fcbingen, T\u00fcbingen, Germany#TAB#","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002248255","display_name":"Nikolas Fechner","orcid":"https://orcid.org/0000-0003-3852-3950"},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Nikolas Fechner","raw_affiliation_strings":["University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","University of T\u00fcbingen, T\u00fcbingen, Germany#TAB#"],"affiliations":[{"raw_affiliation_string":"University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"University of T\u00fcbingen, T\u00fcbingen, Germany#TAB#","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004958444","display_name":"Andreas Zell","orcid":"https://orcid.org/0000-0003-3299-2211"},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"A Zell","raw_affiliation_strings":["University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","University of T\u00fcbingen, T\u00fcbingen, Germany#TAB#"],"affiliations":[{"raw_affiliation_string":"University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"University of T\u00fcbingen, T\u00fcbingen, Germany#TAB#","institution_ids":["https://openalex.org/I8087733"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5066354297"],"corresponding_institution_ids":["https://openalex.org/I8087733"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10905434,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"2","issue":"S1","first_page":null,"last_page":null},"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9799000024795532,"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"}},{"id":"https://openalex.org/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9495000243186951,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pharmacophore","display_name":"Pharmacophore","score":0.9178165197372437},{"id":"https://openalex.org/keywords/substructure","display_name":"Substructure","score":0.7810382843017578},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6856255531311035},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4508601427078247},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3305910527706146},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20358505845069885},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09443485736846924},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.09066060185432434}],"concepts":[{"id":"https://openalex.org/C56173144","wikidata":"https://www.wikidata.org/wiki/Q1539893","display_name":"Pharmacophore","level":2,"score":0.9178165197372437},{"id":"https://openalex.org/C99679407","wikidata":"https://www.wikidata.org/wiki/Q56761637","display_name":"Substructure","level":2,"score":0.7810382843017578},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6856255531311035},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4508601427078247},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3305910527706146},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20358505845069885},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09443485736846924},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.09066060185432434},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-2-s1-p42","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-p42","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P42","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:7bc819dc81c848ab83f08f7c26ef64ba","is_oa":true,"landing_page_url":"https://doaj.org/article/7bc819dc81c848ab83f08f7c26ef64ba","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 2, Iss Suppl 1, p P42 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2867177","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2867177","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-2-s1-p42","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-p42","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P42","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2024502043.pdf","grobid_xml":"https://content.openalex.org/works/W2024502043.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W2025135899","https://openalex.org/W2042110087","https://openalex.org/W2127760066"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W3184587995","https://openalex.org/W2197392606","https://openalex.org/W2943414817","https://openalex.org/W1605005150","https://openalex.org/W3092402433","https://openalex.org/W2716636539","https://openalex.org/W2385923153","https://openalex.org/W2902128418","https://openalex.org/W2511683653"],"abstract_inverted_index":{"The":[0,108,143,169,183,234,275],"generation":[1],"of":[2,15,21,42,48,57,84,87,93,106,116,125,193,201,213,236,251,261,264,297,318,323],"a":[3,7,19,24,67,85,131,151,176,206,241,259,319,339],"pharmacophore":[4,33,114,127,191,247,340],"model":[5,341],"is":[6,29,60,103,224,268,302,327,346],"challenging":[8],"process,":[9,219],"which":[10,134,226],"often":[11],"requires":[12],"the":[13,27,32,39,55,74,104,113,122,126,139,157,167,190,194,199,211,214,217,220,230,237,249,252,262,281,294,298,315,324,331],"interaction":[14],"medicinal":[16],"chemists.":[17],"Given":[18,150],"number":[20,105],"ligands":[22],"for":[23,38,166,189,270,314],"specific":[25],"target,":[26],"aim":[28],"to":[30,62,76,80,138,292,304,337],"identify":[31,81],"patterns":[34,192],"that":[35,54,244,267,311],"are":[36,312],"responsible":[37],"biological":[40,316],"activities":[41],"chemical":[43,58],"compounds.":[44,182],"A":[45],"recent":[46],"study":[47],"optimal":[49],"assignment":[50,56],"methods":[51],"has":[52],"shown":[53],"substructures":[59,92,109],"able":[61,303],"detect":[63],"active":[64,88,94,155,159,171],"compounds":[65,172],"in":[66],"data":[68,152,178],"set":[69,86,153,179],"[1].":[70],"Therefore,":[71,330],"we":[72,96,129,204],"investigated":[73],"possibility":[75],"use":[77],"this":[78],"technique":[79],"key":[82,309],"features":[83,310],"compounds.\r\n\r\nTo":[89],"determine":[90,293],"important":[91,313],"compounds,":[95,156],"integrated":[97,130],"n":[98,102,187],"weight":[99,136,242,250],"factors,":[100],"where":[101],"substructures.":[107],"were":[110,173],"defined":[111,141],"using":[112],"definitions":[115],"Phase":[117],"3.0":[118],"[2].":[119],"To":[120,197],"define":[121],"individual":[123],"weights":[124,188,212],"patterns,":[128],"genetic":[132,184,238],"algorithm":[133,185,239],"assigns":[135,245],"factors":[137],"previously":[140],"patterns.":[142],"experimental":[144],"setup":[145],"was":[146,161,240,278],"designed":[147],"as":[148,163],"follows:":[149],"with":[154,210],"most":[158],"compound":[160],"selected":[162],"query":[164,195,208,276],"structure":[165,277,285,326,345],"experiment.":[168],"remaining":[170],"inserted":[174],"into":[175],"background":[177],"containing":[180],"inactive":[181],"evolved":[186],"structure.":[196],"evaluate":[198],"fitness":[200],"an":[202],"individual,":[203],"performed":[205],"single":[207],"screening":[209,273],"individual.":[215],"During":[216],"optimization":[218],"BEDROC":[221],"score":[222],"[3]":[223],"optimized":[225],"puts":[227],"emphasis":[228],"on":[229,258],"early":[231],"recognition":[232],"performance.":[233],"result":[235],"vector":[243],"each":[246],"feature":[248],"best":[253],"individual.\r\n\r\nWe":[254],"evaluated":[255],"our":[256],"approach":[257],"subset":[260],"Directory":[263],"Useful":[265],"Decoys":[266],"suitable":[269],"ligand-based":[271],"virtual":[272],"[1][4].":[274],"extracted":[279],"from":[280],"same":[282],"complexed":[283],"crystal":[284],"used":[286,336],"by":[287],"Huang":[288],"et":[289],"al.":[290],"[4]":[291],"binding":[295],"site":[296],"protein.\r\n\r\nThe":[299],"presented":[300],"method":[301,332],"provide":[305],"valuable":[306],"information":[307,322],"about":[308],"activity":[317],"compound.":[320],"Additionally,":[321],"protein":[325,344],"not":[328],"needed.":[329],"can":[333],"also":[334],"be":[335],"derive":[338],"if":[342],"no":[343],"available":[347],"(e.g.":[348],"GPCRs).":[349]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
