{"id":"https://openalex.org/W2028920034","doi":"https://doi.org/10.1021/ci200442h","title":"Modeling Flexible Pharmacophores with Distance Geometry, Scoring, and Bound Stretching","display_name":"Modeling Flexible Pharmacophores with Distance Geometry, Scoring, and Bound Stretching","publication_year":2012,"publication_date":"2012-01-11","ids":{"openalex":"https://openalex.org/W2028920034","doi":"https://doi.org/10.1021/ci200442h","mag":"2028920034","pmid":"https://pubmed.ncbi.nlm.nih.gov/22235879"},"language":"en","primary_location":{"id":"doi:10.1021/ci200442h","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200442h","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/A5074323078","display_name":"Michael Binns","orcid":"https://orcid.org/0000-0002-6881-0048"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Michael Binns","raw_affiliation_strings":["School\rof Chemical Engineering and Analytical Science and \u2021Manchester Interdisciplinary Biocentre, University of Manchester, Manchester\rM13 9PL, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School\rof Chemical Engineering and Analytical Science and \u2021Manchester Interdisciplinary Biocentre, University of Manchester, Manchester\rM13 9PL, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016167248","display_name":"Sam P. de Visser","orcid":"https://orcid.org/0000-0002-2620-8788"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sam P. de Visser","raw_affiliation_strings":["School\rof Chemical Engineering and Analytical Science and \u2021Manchester Interdisciplinary Biocentre, University of Manchester, Manchester\rM13 9PL, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School\rof Chemical Engineering and Analytical Science and \u2021Manchester Interdisciplinary Biocentre, University of Manchester, Manchester\rM13 9PL, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042774766","display_name":"Constantinos Theodoropoulos","orcid":"https://orcid.org/0000-0003-3249-0422"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Constantinos Theodoropoulos","raw_affiliation_strings":["School\rof Chemical Engineering and Analytical Science and \u2021Manchester Interdisciplinary Biocentre, University of Manchester, Manchester\rM13 9PL, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School\rof Chemical Engineering and Analytical Science and \u2021Manchester Interdisciplinary Biocentre, University of Manchester, Manchester\rM13 9PL, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5074323078"],"corresponding_institution_ids":["https://openalex.org/I28407311"],"apc_list":null,"apc_paid":null,"fwci":1.0366,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.77098895,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"52","issue":"2","first_page":"577","last_page":"588"},"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9884999990463257,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9786999821662903,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pharmacophore","display_name":"Pharmacophore","score":0.9889655113220215},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6058616638183594},{"id":"https://openalex.org/keywords/upper-and-lower-bounds","display_name":"Upper and lower bounds","score":0.547969400882721},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.44954273104667664},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4486553370952606},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3658820688724518},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.33552563190460205},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3087625205516815},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2863580584526062},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.19258782267570496}],"concepts":[{"id":"https://openalex.org/C56173144","wikidata":"https://www.wikidata.org/wiki/Q1539893","display_name":"Pharmacophore","level":2,"score":0.9889655113220215},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6058616638183594},{"id":"https://openalex.org/C77553402","wikidata":"https://www.wikidata.org/wiki/Q13222579","display_name":"Upper and lower bounds","level":2,"score":0.547969400882721},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.44954273104667664},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4486553370952606},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3658820688724518},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.33552563190460205},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3087625205516815},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2863580584526062},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.19258782267570496},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"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/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001696","descriptor_name":"Biomechanical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001696","descriptor_name":"Biomechanical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001696","descriptor_name":"Biomechanical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D008722","descriptor_name":"Methods","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008722","descriptor_name":"Methods","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008722","descriptor_name":"Methods","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":"D013917","descriptor_name":"Thrombin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013917","descriptor_name":"Thrombin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013917","descriptor_name":"Thrombin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci200442h","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200442h","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:22235879","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22235879","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},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/69792de0-69f1-4afb-92c3-d26bfd20a03a","is_oa":false,"landing_page_url":"https://research.manchester.ac.uk/en/publications/69792de0-69f1-4afb-92c3-d26bfd20a03a","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Binns, M, De Visser, S P & Theodoropoulos, C 2012, 'Modeling flexible pharmacophores with distance geometry, scoring, and bound stretching.', Journal of Chemical Information and Modeling, vol. 52, no. 2, pp. 577-588. https://doi.org/10.1021/ci200442h","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.41999998688697815,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1491938055","https://openalex.org/W1546015235","https://openalex.org/W1967449361","https://openalex.org/W1972368129","https://openalex.org/W1978705163","https://openalex.org/W1979537657","https://openalex.org/W1987910020","https://openalex.org/W1988832667","https://openalex.org/W1994037959","https://openalex.org/W1995746750","https://openalex.org/W1995852445","https://openalex.org/W1997986227","https://openalex.org/W1999491936","https://openalex.org/W2002559252","https://openalex.org/W2002755329","https://openalex.org/W2003861094","https://openalex.org/W2007348965","https://openalex.org/W2014231697","https://openalex.org/W2022437298","https://openalex.org/W2023752424","https://openalex.org/W2035127771","https://openalex.org/W2039047003","https://openalex.org/W2046311259","https://openalex.org/W2049620183","https://openalex.org/W2050251045","https://openalex.org/W2052696550","https://openalex.org/W2053333781","https://openalex.org/W2077973224","https://openalex.org/W2081301773","https://openalex.org/W2090971258","https://openalex.org/W2093814695","https://openalex.org/W2094839792","https://openalex.org/W2113221321","https://openalex.org/W2116007667","https://openalex.org/W2130479394","https://openalex.org/W2130844078","https://openalex.org/W2136315807","https://openalex.org/W2139665064","https://openalex.org/W2155365721"],"related_works":["https://openalex.org/W42225299","https://openalex.org/W2943414817","https://openalex.org/W2197392606","https://openalex.org/W1605005150","https://openalex.org/W3184587995","https://openalex.org/W3092402433","https://openalex.org/W2716636539","https://openalex.org/W2902128418","https://openalex.org/W2385923153","https://openalex.org/W2394308601"],"abstract_inverted_index":{"The":[0,73,122],"study":[1,176,202],"of":[2,5,17,46,61,69,84,99,106,114,139,171,209],"pharmacophores,":[3],"i.e.,":[4],"common":[6,132],"features":[7],"between":[8,82,104],"different":[9,88],"ligands,":[10],"is":[11,26,150,177],"important":[12],"for":[13],"the":[14,70,79,87,100,137,144,154,157,168,217],"quantitative":[15],"identification":[16,223],"\"compatible\"":[18],"enzymes":[19],"and":[20,116,186],"binding":[21,191],"species.":[22],"A":[23,147,174,199],"pharmacophore-based":[24],"technique":[25],"developed":[27],"that":[28],"combines":[29],"multiple":[30],"conformations":[31,48],"with":[32,50,156,167,220],"a":[33,44,51,112,129,195,207],"distance":[34,62,102,118,140],"geometry":[35],"method":[36,219],"to":[37,58,109,142,152,188,215],"create":[38,59],"flexible":[39,123,182,204],"pharmacophore":[40,124,197,222],"representations.":[41],"It":[42],"uses":[43,136],"set":[45,113,208],"low-energy":[47,71,89],"combined":[49],"new":[52,218],"process":[53],"we":[54,95],"call":[55],"bound":[56],"stretching":[57],"sets":[60,105],"bounds,":[63],"which":[64,135,180],"contain":[65],"all":[66],"or":[67],"most":[68],"conformations.":[72,90],"bounds":[74,119,141],"can":[75,96,125],"be":[76,126,164],"obtained":[77],"using":[78,128],"exact":[80],"distances":[81],"pairs":[83],"atoms":[85],"from":[86,206],"To":[91],"avoid":[92],"missing":[93],"conformations,":[94],"take":[97],"advantage":[98],"triangle":[101],"inequality":[103],"three":[107],"points":[108],"logically":[110],"expand":[111],"upper":[115],"lower":[117],"(bound":[120],"stretching).":[121],"found":[127],"3-D":[130,181],"maximal":[131],"subgraph":[133],"method,":[134],"overlap":[138,159],"determine":[143],"overlapping":[145,172],"structure.":[146],"scoring":[148],"routine":[149],"implemented":[151],"select":[153],"substructures":[155],"largest":[158],"because":[160],"there":[161],"will":[162],"typically":[163],"many":[165],"overlaps":[166],"maximum":[169],"number":[170],"bounds.":[173],"case":[175,201],"presented":[178],"in":[179],"pharmacophores":[183,205],"are":[184,213],"generated":[185],"used":[187,214],"eliminate":[189],"potential":[190],"species":[192],"identified":[193],"by":[194],"2-D":[196],"method.":[198],"second":[200],"creates":[203],"thrombin":[210],"ligands.":[211],"These":[212],"compare":[216],"existing":[221],"software.":[224]},"counts_by_year":[{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
