{"id":"https://openalex.org/W2087825005","doi":"https://doi.org/10.1021/ci900199e","title":"Predicting Multiple Ligand Binding Modes Using Self-Consistent Pharmacophore Hypotheses","display_name":"Predicting Multiple Ligand Binding Modes Using Self-Consistent Pharmacophore Hypotheses","publication_year":2009,"publication_date":"2009-08-27","ids":{"openalex":"https://openalex.org/W2087825005","doi":"https://doi.org/10.1021/ci900199e","mag":"2087825005","pmid":"https://pubmed.ncbi.nlm.nih.gov/19711952"},"language":"en","primary_location":{"id":"doi:10.1021/ci900199e","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci900199e","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/A5064707937","display_name":"Izhar Wallach","orcid":"https://orcid.org/0000-0002-7212-3048"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Izhar Wallach","raw_affiliation_strings":["Department of Computer Science, Donnelly Centre for Cellular and Biomolecular Research, and Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Donnelly Centre for Cellular and Biomolecular Research, and Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071031693","display_name":"Ryan Lilien","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Ryan Lilien","raw_affiliation_strings":["Department of Computer Science, Donnelly Centre for Cellular and Biomolecular Research, and Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Donnelly Centre for Cellular and Biomolecular Research, and Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5064707937","https://openalex.org/A5071031693"],"corresponding_institution_ids":["https://openalex.org/I185261750"],"apc_list":null,"apc_paid":null,"fwci":1.4182,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.8180771,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"49","issue":"9","first_page":"2116","last_page":"2128"},"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":0.982200026512146,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9657999873161316,"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/pharmacophore","display_name":"Pharmacophore","score":0.9135683178901672},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4874746799468994},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44459328055381775},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.42509356141090393},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35778069496154785},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.25281184911727905},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2240542769432068},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12466537952423096},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.11870074272155762}],"concepts":[{"id":"https://openalex.org/C56173144","wikidata":"https://www.wikidata.org/wiki/Q1539893","display_name":"Pharmacophore","level":2,"score":0.9135683178901672},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4874746799468994},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44459328055381775},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.42509356141090393},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35778069496154785},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.25281184911727905},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2240542769432068},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12466537952423096},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.11870074272155762}],"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":"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":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci900199e","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci900199e","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:19711952","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19711952","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":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.7400000095367432}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1506806321","https://openalex.org/W1970651561","https://openalex.org/W1974638435","https://openalex.org/W1981076832","https://openalex.org/W1981608946","https://openalex.org/W1986240377","https://openalex.org/W2006322600","https://openalex.org/W2026949262","https://openalex.org/W2049917593","https://openalex.org/W2049961577","https://openalex.org/W2050992060","https://openalex.org/W2051594610","https://openalex.org/W2055410316","https://openalex.org/W2068017935","https://openalex.org/W2082287671","https://openalex.org/W2085313140","https://openalex.org/W2090971258","https://openalex.org/W2093426296","https://openalex.org/W2109632148","https://openalex.org/W2114779636","https://openalex.org/W2121895929","https://openalex.org/W2127758174","https://openalex.org/W2130479394","https://openalex.org/W2143482176","https://openalex.org/W2146940292","https://openalex.org/W2152964937","https://openalex.org/W2165232124","https://openalex.org/W2494768458","https://openalex.org/W2949504121","https://openalex.org/W6751306947"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834","https://openalex.org/W2770470780"],"abstract_inverted_index":{"The":[0,144,191],"ability":[1],"to":[2,65,85,109,123,139,165,201,211,229,265],"predict":[3,126],"ligand":[4],"binding":[5,49,76,111,128,162,196,286],"modes":[6,197],"without":[7],"the":[8,17,33,47,127,141,149,217,224,227,269,279],"aid":[9],"of":[10,19,82,117,133,158,194,205,226,261,278,289],"wet-lab":[11,36],"experiments":[12],"may":[13,283],"accelerate":[14],"and":[15,100,239,242,282],"reduce":[16],"cost":[18],"drug":[20],"discovery":[21],"research.":[22],"Despite":[23],"significant":[24],"recent":[25],"progress,":[26],"virtual":[27,102,271,290],"screening":[28,103],"has":[29,44],"not":[30],"yet":[31],"eliminated":[32],"need":[34],"for":[35,79,130,187,252],"experiments.":[37,292],"For":[38],"example,":[39],"after":[40],"a":[41,71,80,88,114,131,156,168,177,203,212,258],"lead":[42,67],"compound":[43],"been":[45],"identified,":[46],"precise":[48],"mode":[50,77,129,287],"is":[51,62,92,146,276],"still":[52],"typically":[53],"determined":[54],"by":[55],"experimental":[56],"structural":[57,60],"biology.":[58],"This":[59,256],"knowledge":[61],"then":[63,199],"employed":[64],"guide":[66],"optimization.":[68],"We":[69,220],"present":[70],"step":[72],"toward":[73],"improving":[74],"protein-ligand":[75,185],"prediction":[78,288],"set":[81,132,157,204],"ligands":[83,112,134,163],"known":[84,138,189],"interact":[86],"with":[87,209,245],"common":[89],"protein.":[90,143],"There":[91],"thus":[93],"an":[94,246],"important":[95],"distinction":[96],"between":[97],"this":[98],"work":[99],"traditional":[101,106,170,184],"algorithms.":[104],"Whereas":[105],"approaches":[107],"attempt":[108],"identify":[110,202],"from":[113,216],"large":[115],"database":[116],"available":[118],"compounds,":[119],"our":[120],"approach":[121,145],"aims":[122],"more":[124,169],"accurately":[125],"which":[135,161],"are":[136,198],"already":[137],"bind":[140],"target":[142],"based":[147],"on":[148],"hypothesis":[150],"that":[151],"each":[152,188],"active":[153],"site":[154],"contains":[155],"interaction":[159,173],"points":[160,174],"tend":[164],"exploit.":[166],"In":[167],"context,":[171],"these":[172],"make":[175],"up":[176],"pharmacophoric":[178,213],"map.":[179],"Our":[180,274],"algorithm":[181,228,275],"first":[182],"performs":[183],"docking":[186,272,280,291],"binder.":[190],"ranked":[192],"lists":[193],"candidate":[195],"evaluated":[200],"poses":[206],"maximally":[207],"self-consistent":[208],"respect":[210],"map":[214],"generated":[215],"same":[218],"poses.":[219],"have":[221],"extensively":[222],"demonstrated":[223],"application":[225],"four":[230],"protein":[231],"systems":[232],"(thrombin,":[233],"cyclin-dependent":[234],"kinase":[235],"2,":[236],"dihydrofolate":[237],"reductase,":[238],"HIV-1":[240],"protease)":[241],"attained":[243],"predictions":[244],"average":[247],"RMSD":[248,267],"<":[249],"2.5":[250],"A":[251,263],"all":[253],"tested":[254],"systems.":[255],"represents":[257],"typical":[259],"improvement":[260],"0.5-1.0":[262],"(up":[264],"25%)":[266],"over":[268],"naive":[270],"predictions.":[273],"independent":[277],"method":[281],"significantly":[284],"improve":[285]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
