{"id":"https://openalex.org/W2024097662","doi":"https://doi.org/10.1021/ci025605o","title":"CLIP:\u2009 Similarity Searching of 3D Databases Using Clique Detection","display_name":"CLIP:\u2009 Similarity Searching of 3D Databases Using Clique Detection","publication_year":2003,"publication_date":"2003-02-28","ids":{"openalex":"https://openalex.org/W2024097662","doi":"https://doi.org/10.1021/ci025605o","mag":"2024097662","pmid":"https://pubmed.ncbi.nlm.nih.gov/12653507"},"language":"en","primary_location":{"id":"doi:10.1021/ci025605o","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci025605o","pdf_url":null,"source":{"id":"https://openalex.org/S171559003","display_name":"Journal of Chemical Information and Computer Sciences","issn_l":"0095-2338","issn":["0095-2338","1520-5142"],"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 Computer Sciences","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/A5070996258","display_name":"Nicholas P. Rhodes","orcid":"https://orcid.org/0000-0002-5173-7032"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Nicholas Rhodes","raw_affiliation_strings":["Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102885255","display_name":"Peter Willett","orcid":"https://orcid.org/0000-0003-4591-7173"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Peter Willett","raw_affiliation_strings":["University of  Sheffield"],"affiliations":[{"raw_affiliation_string":"University of  Sheffield","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016940802","display_name":"Alain Calvet","orcid":null},"institutions":[{"id":"https://openalex.org/I180857899","display_name":"Pfizer (United States)","ror":"https://ror.org/01xdqrp08","country_code":"US","type":"company","lineage":["https://openalex.org/I180857899"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alain Calvet","raw_affiliation_strings":["Pfizer"],"affiliations":[{"raw_affiliation_string":"Pfizer","institution_ids":["https://openalex.org/I180857899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076900353","display_name":"James B. Dunbar","orcid":"https://orcid.org/0009-0008-6752-1421"},"institutions":[{"id":"https://openalex.org/I4210147708","display_name":"Institute of Medicinal Plant Development","ror":"https://ror.org/052nj8f19","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210141683","https://openalex.org/I4210147708"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"James B. Dunbar","raw_affiliation_strings":["Medicinal Chemistry"],"affiliations":[{"raw_affiliation_string":"Medicinal Chemistry","institution_ids":["https://openalex.org/I4210147708"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070728610","display_name":"Christine Humblet","orcid":"https://orcid.org/0000-0003-1775-4426"},"institutions":[{"id":"https://openalex.org/I180857899","display_name":"Pfizer (United States)","ror":"https://ror.org/01xdqrp08","country_code":"US","type":"company","lineage":["https://openalex.org/I180857899"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christine Humblet","raw_affiliation_strings":["Pfizer"],"affiliations":[{"raw_affiliation_string":"Pfizer","institution_ids":["https://openalex.org/I180857899"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5070996258"],"corresponding_institution_ids":["https://openalex.org/I91136226"],"apc_list":null,"apc_paid":null,"fwci":2.9094,"has_fulltext":false,"cited_by_count":50,"citation_normalized_percentile":{"value":0.90954211,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"43","issue":"2","first_page":"443","last_page":"448"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994000196456909,"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":0.9994000196456909,"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/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9969000220298767,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.978600025177002,"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/clique","display_name":"Clique","score":0.8200112581253052},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.7888356447219849},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6595374941825867},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.625499963760376},{"id":"https://openalex.org/keywords/pharmacophore","display_name":"Pharmacophore","score":0.5806978344917297},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5474735498428345},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.47840723395347595},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4619145393371582},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3788948655128479},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.36658820509910583},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.34305649995803833},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29358187317848206},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23092618584632874},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.20002591609954834},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.1611163318157196},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.09373712539672852}],"concepts":[{"id":"https://openalex.org/C2777035058","wikidata":"https://www.wikidata.org/wiki/Q1662634","display_name":"Clique","level":2,"score":0.8200112581253052},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.7888356447219849},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6595374941825867},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.625499963760376},{"id":"https://openalex.org/C56173144","wikidata":"https://www.wikidata.org/wiki/Q1539893","display_name":"Pharmacophore","level":2,"score":0.5806978344917297},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5474735498428345},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.47840723395347595},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4619145393371582},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3788948655128479},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.36658820509910583},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.34305649995803833},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29358187317848206},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23092618584632874},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.20002591609954834},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.1611163318157196},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.09373712539672852},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","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/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1021/ci025605o","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci025605o","pdf_url":null,"source":{"id":"https://openalex.org/S171559003","display_name":"Journal of Chemical Information and Computer Sciences","issn_l":"0095-2338","issn":["0095-2338","1520-5142"],"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 Computer Sciences","raw_type":"journal-article"},{"id":"pmid:12653507","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12653507","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 computer sciences","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":0.8500000238418579}],"awards":[],"funders":[{"id":"https://openalex.org/F4320307765","display_name":"Pfizer","ror":"https://ror.org/01xdqrp08"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1518367201","https://openalex.org/W1575639801","https://openalex.org/W1963723282","https://openalex.org/W1969714023","https://openalex.org/W1970936511","https://openalex.org/W1978184203","https://openalex.org/W2005685204","https://openalex.org/W2046509566","https://openalex.org/W2056177030","https://openalex.org/W2059864723","https://openalex.org/W2068154266","https://openalex.org/W2073329308","https://openalex.org/W2075986011","https://openalex.org/W2084541152","https://openalex.org/W2086664575","https://openalex.org/W2096023298","https://openalex.org/W2096729078","https://openalex.org/W2103238395","https://openalex.org/W2120540345"],"related_works":["https://openalex.org/W2000397010","https://openalex.org/W2115078847","https://openalex.org/W2062768126","https://openalex.org/W2080809815","https://openalex.org/W2969563261","https://openalex.org/W2061401330","https://openalex.org/W3041915240","https://openalex.org/W2055137136","https://openalex.org/W2167386965","https://openalex.org/W1580389218"],"abstract_inverted_index":{"This":[0,66],"paper":[1],"describes":[2],"a":[3,28,37,74],"program":[4],"for":[5],"3D":[6],"similarity":[7,52],"searching,":[8],"called":[9],"CLIP":[10],"(for":[11],"Candidate":[12],"Ligand":[13],"Identification":[14],"Program),":[15],"that":[16,30,73,81],"uses":[17],"the":[18,44,51,60,71,92,96,105,108],"Bron-Kerbosch":[19],"clique":[20],"detection":[21],"algorithm":[22],"to":[23,79,113],"find":[24],"those":[25],"structures":[26,33,55],"in":[27,34],"file":[29],"have":[31],"large":[32],"common":[35],"with":[36,100],"target":[38],"structure.":[39],"Structures":[40],"are":[41],"characterized":[42],"by":[43],"geometric":[45],"arrangement":[46],"of":[47,59,83,95,110],"pharmacophore":[48],"points":[49],"and":[50,62,107],"between":[53],"two":[54],"calculated":[56],"using":[57],"modifications":[58],"Simpson":[61],"Tanimoto":[63],"association":[64],"coefficients.":[65],"modification":[67],"takes":[68],"into":[69],"account":[70],"fact":[72],"distance":[75],"tolerance":[76],"is":[77],"required":[78],"ensure":[80],"pairs":[82],"interatomic":[84],"distances":[85],"can":[86],"be":[87],"regarded":[88],"as":[89],"equivalent":[90],"during":[91],"clique-construction":[93],"stage":[94],"matching":[97],"algorithm.":[98],"Experiments":[99],"HIV":[101],"assay":[102],"data":[103],"demonstrate":[104],"effectiveness":[106],"efficiency":[109],"this":[111],"approach":[112],"virtual":[114],"screening.":[115]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":4}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
