{"id":"https://openalex.org/W2025730034","doi":"https://doi.org/10.1021/ci800310f","title":"Improving the Accuracy of an Affinity Prediction Method by Using Statistics on Shape Complementarity between Proteins","display_name":"Improving the Accuracy of an Affinity Prediction Method by Using Statistics on Shape Complementarity between Proteins","publication_year":2009,"publication_date":"2009-02-10","ids":{"openalex":"https://openalex.org/W2025730034","doi":"https://doi.org/10.1021/ci800310f","mag":"2025730034","pmid":"https://pubmed.ncbi.nlm.nih.gov/19434902"},"language":"en","primary_location":{"id":"doi:10.1021/ci800310f","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci800310f","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/A5081648935","display_name":"Tatsuya Yoshikawa","orcid":"https://orcid.org/0000-0002-4764-7368"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tatsuya Yoshikawa","raw_affiliation_strings":["Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan, and Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan, and Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan","institution_ids":["https://openalex.org/I73613424","https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102098579","display_name":"Koki Tsukamoto","orcid":null},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Koki Tsukamoto","raw_affiliation_strings":["Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan, and Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan, and Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan","institution_ids":["https://openalex.org/I73613424","https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058948456","display_name":"Yuichiro Hourai","orcid":null},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuichiro Hourai","raw_affiliation_strings":["Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan, and Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan, and Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan","institution_ids":["https://openalex.org/I73613424","https://openalex.org/I98285908"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076215084","display_name":"Kazuhiko Fukui","orcid":"https://orcid.org/0000-0002-2482-8481"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kazuhiko Fukui","raw_affiliation_strings":["Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan, and Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan, and Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan","institution_ids":["https://openalex.org/I73613424","https://openalex.org/I98285908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5076215084"],"corresponding_institution_ids":["https://openalex.org/I73613424","https://openalex.org/I98285908"],"apc_list":null,"apc_paid":null,"fwci":1.2324,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.78024177,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"49","issue":"3","first_page":"693","last_page":"703"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9965999722480774,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9965999722480774,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9872999787330627,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9854000210762024,"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/complementarity","display_name":"Complementarity (molecular biology)","score":0.8168760538101196},{"id":"https://openalex.org/keywords/receiver-operating-characteristic","display_name":"Receiver operating characteristic","score":0.607367753982544},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.48665720224380493},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.43783220648765564},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.43727102875709534},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.4267085790634155},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.41000908613204956},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3943064212799072},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3685073256492615},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3461982309818268},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33249008655548096},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2678379416465759},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15804904699325562},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08735582232475281}],"concepts":[{"id":"https://openalex.org/C202269582","wikidata":"https://www.wikidata.org/wiki/Q2644277","display_name":"Complementarity (molecular biology)","level":2,"score":0.8168760538101196},{"id":"https://openalex.org/C58471807","wikidata":"https://www.wikidata.org/wiki/Q327120","display_name":"Receiver operating characteristic","level":2,"score":0.607367753982544},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.48665720224380493},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.43783220648765564},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.43727102875709534},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.4267085790634155},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.41000908613204956},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3943064212799072},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3685073256492615},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3461982309818268},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33249008655548096},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2678379416465759},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15804904699325562},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08735582232475281},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci800310f","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci800310f","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:19434902","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19434902","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":[],"funders":[{"id":"https://openalex.org/F4320322832","display_name":"University of Tokyo","ror":"https://ror.org/057zh3y96"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W196260823","https://openalex.org/W1850562386","https://openalex.org/W1896254721","https://openalex.org/W1946659263","https://openalex.org/W1965410913","https://openalex.org/W1966421023","https://openalex.org/W1968713350","https://openalex.org/W1977186059","https://openalex.org/W1983036219","https://openalex.org/W1994803330","https://openalex.org/W2004360551","https://openalex.org/W2006124679","https://openalex.org/W2014744153","https://openalex.org/W2015226105","https://openalex.org/W2031772330","https://openalex.org/W2040941311","https://openalex.org/W2041206203","https://openalex.org/W2061758347","https://openalex.org/W2065304353","https://openalex.org/W2071510805","https://openalex.org/W2075424513","https://openalex.org/W2075770210","https://openalex.org/W2079818352","https://openalex.org/W2084700070","https://openalex.org/W2086224494","https://openalex.org/W2088422296","https://openalex.org/W2104315543","https://openalex.org/W2105438341","https://openalex.org/W2111387452","https://openalex.org/W2112322820","https://openalex.org/W2113654464","https://openalex.org/W2129414710","https://openalex.org/W2129454543","https://openalex.org/W2134825371","https://openalex.org/W2135737340","https://openalex.org/W2137321308","https://openalex.org/W2157991822","https://openalex.org/W2166558964","https://openalex.org/W2168989922","https://openalex.org/W2406745763","https://openalex.org/W4237572013"],"related_works":["https://openalex.org/W2521519254","https://openalex.org/W3139833644","https://openalex.org/W3123110765","https://openalex.org/W4383553409","https://openalex.org/W2212953222","https://openalex.org/W2104948296","https://openalex.org/W1735800226","https://openalex.org/W4385649027","https://openalex.org/W4285172739","https://openalex.org/W2593903992"],"abstract_inverted_index":{"To":[0,193],"elucidate":[1],"the":[2,25,34,64,102,105,136,144,168,195,201],"partners":[3],"in":[4,38,183,188,197],"protein-protein":[5],"interactions":[6],"(PPIs),":[7],"we":[8,72,118,199],"previously":[9],"proposed":[10],"an":[11,133],"affinity":[12,16,108],"prediction":[13,19,151],"method":[14,50],"called":[15,51],"evaluation":[17,42],"and":[18,67,89,104,132,185,209],"(AEP),":[20],"which":[21],"is":[22],"based":[23,95],"on":[24,96],"shape":[26,40],"complementarity":[27,41],"characteristics":[28],"between":[29],"proteins.":[30],"The":[31],"structures":[32],"of":[33,107,113,138,143,171,190,203,205,210],"protein":[35,82,165],"complexes":[36,88,162,173],"obtained":[37,119],"our":[39],"were":[43,174],"selected":[44],"by":[45,141],"a":[46,74,111,154],"newly":[47],"developed":[48],"clustering":[49],"grouping.":[52],"Our":[53],"previous":[54],"experiments":[55],"showed":[56],"that":[57,61,157],"AEP":[58,146,204],"gave":[59],"accuracies":[60],"differed":[62],"with":[63,177],"data":[65,75,207],"composition":[66],"scale.":[68],"In":[69],"this":[70],"study,":[71],"set":[73],"scale":[76],"(84":[77],"x":[78],"84":[79,85,164],"=":[80],"7056":[81],"pairs)":[83],"including":[84],"biologically":[86],"relevant":[87],"then":[90],"designed":[91],"225":[92],"parameter":[93],"sets":[94,208],"four":[97],"key":[98],"parameters":[99],"related":[100],"to":[101,149],"grouping":[103],"calculation":[106],"scores.":[109,218],"As":[110],"result":[112],"receiver":[114],"operating":[115],"characteristic":[116],"analysis,":[117],"27.4%":[120],"sensitivity":[121],"(=":[122],"recall),":[123],"91.0%":[124],"specificity,":[125],"3.5%":[126],"precision,":[127],"90.2%":[128],"accuracy,":[129],"6.3%":[130],"F-measure(max),":[131],"area":[134],"under":[135],"curve":[137],"0.585.":[139],"Chiefly":[140],"optimization":[142],"grouping,":[145],"was":[147],"able":[148],"provide":[150],"accuracy":[152,179,198],"for":[153],"maximum":[155],"F-measure":[156],"statistically":[158],"distinguished":[159],"23":[160],"target":[161],"among":[163],"pairs.":[166],"Moreover,":[167],"active":[169],"sites":[170],"these":[172],"successfully":[175],"predicted":[176],"high":[178],"(i.e.,":[180],"2.37":[181],"angstroms":[182,187],"1CGI":[184],"2.38":[186],"1PPE)":[189],"interface":[191],"RMSD.":[192],"assess":[194],"improvement":[196],"compared":[200],"results":[202],"different":[206],"tentative":[211],"methods":[212],"using":[213],"ZDOCK":[214],"3.0.1":[215],"or":[216],"ZRANK":[217]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
