{"id":"https://openalex.org/W3100260541","doi":"https://doi.org/10.1142/s0219720020500420","title":"Protein\u2013protein interaction site prediction using random forest proximity distance","display_name":"Protein\u2013protein interaction site prediction using random forest proximity distance","publication_year":2020,"publication_date":"2020-09-17","ids":{"openalex":"https://openalex.org/W3100260541","doi":"https://doi.org/10.1142/s0219720020500420","mag":"3100260541","pmid":"https://pubmed.ncbi.nlm.nih.gov/33215966"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720020500420","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720020500420","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","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/A5120218367","display_name":"Zhijun Qiu","orcid":"https://orcid.org/0000-0001-8197-9975"},"institutions":[{"id":"https://openalex.org/I167383011","display_name":"Henan University of Science and Technology","ror":"https://ror.org/05d80kz58","country_code":"CN","type":"education","lineage":["https://openalex.org/I167383011"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhijun Qiu","raw_affiliation_strings":["College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, P.\u00a0R.\u00a0China","Henan Engineering Research Center of Food Microbiology, Luoyang 471023, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, P.\u00a0R.\u00a0China","institution_ids":["https://openalex.org/I167383011"]},{"raw_affiliation_string":"Henan Engineering Research Center of Food Microbiology, Luoyang 471023, P. R. China","institution_ids":["https://openalex.org/I167383011"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101787362","display_name":"Qing-Jie Liu","orcid":"https://orcid.org/0000-0002-7406-7414"},"institutions":[{"id":"https://openalex.org/I167383011","display_name":"Henan University of Science and Technology","ror":"https://ror.org/05d80kz58","country_code":"CN","type":"education","lineage":["https://openalex.org/I167383011"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingjie Liu","raw_affiliation_strings":["College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, P.\u00a0R.\u00a0China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, P.\u00a0R.\u00a0China","institution_ids":["https://openalex.org/I167383011"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I167383011"],"apc_list":null,"apc_paid":null,"fwci":0.3336,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.58209807,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"19","issue":"01","first_page":"2050042","last_page":"2050042"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998000264167786,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998000264167786,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9988999962806702,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9952999949455261,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/mahalanobis-distance","display_name":"Mahalanobis distance","score":0.9406682848930359},{"id":"https://openalex.org/keywords/random-forest","display_name":"Random forest","score":0.7568654417991638},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.6022568941116333},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5721016526222229},{"id":"https://openalex.org/keywords/test-set","display_name":"Test set","score":0.5666761994361877},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5091044306755066},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.49351441860198975},{"id":"https://openalex.org/keywords/pearson-product-moment-correlation-coefficient","display_name":"Pearson product-moment correlation coefficient","score":0.48914363980293274},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.48699861764907837},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.4760322868824005},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4244579076766968},{"id":"https://openalex.org/keywords/iterative-method","display_name":"Iterative method","score":0.4107336699962616},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40475326776504517},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.387716144323349},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38304346799850464},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.37694358825683594}],"concepts":[{"id":"https://openalex.org/C1921717","wikidata":"https://www.wikidata.org/wiki/Q1334846","display_name":"Mahalanobis distance","level":2,"score":0.9406682848930359},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.7568654417991638},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.6022568941116333},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5721016526222229},{"id":"https://openalex.org/C169903167","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Test set","level":2,"score":0.5666761994361877},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5091044306755066},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.49351441860198975},{"id":"https://openalex.org/C55078378","wikidata":"https://www.wikidata.org/wiki/Q1136628","display_name":"Pearson product-moment correlation coefficient","level":2,"score":0.48914363980293274},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.48699861764907837},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.4760322868824005},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4244579076766968},{"id":"https://openalex.org/C159694833","wikidata":"https://www.wikidata.org/wiki/Q2321565","display_name":"Iterative method","level":2,"score":0.4107336699962616},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40475326776504517},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.387716144323349},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38304346799850464},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37694358825683594},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"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/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720020500420","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720020500420","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:33215966","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33215966","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 bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.7099999785423279}],"awards":[{"id":"https://openalex.org/G3959264414","display_name":null,"funder_award_id":"31870093","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6080347058","display_name":null,"funder_award_id":"U1404307","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W582864414","https://openalex.org/W1966090011","https://openalex.org/W1973964562","https://openalex.org/W1979648586","https://openalex.org/W2008708467","https://openalex.org/W2021041804","https://openalex.org/W2021170902","https://openalex.org/W2031494645","https://openalex.org/W2057813163","https://openalex.org/W2070506154","https://openalex.org/W2072284383","https://openalex.org/W2088038235","https://openalex.org/W2107432340","https://openalex.org/W2109553965","https://openalex.org/W2118737745","https://openalex.org/W2125507227","https://openalex.org/W2148219066","https://openalex.org/W2162682281","https://openalex.org/W2163879391","https://openalex.org/W2166735471","https://openalex.org/W2201036927","https://openalex.org/W2750640312","https://openalex.org/W2911964244"],"related_works":["https://openalex.org/W4382795578","https://openalex.org/W2355463328","https://openalex.org/W2402648945","https://openalex.org/W1431147547","https://openalex.org/W2771741613","https://openalex.org/W2055761197","https://openalex.org/W2053213469","https://openalex.org/W2057608111","https://openalex.org/W2793032185","https://openalex.org/W4363647452"],"abstract_inverted_index":{"A":[0],"front-end":[1],"method":[2,90,195],"based":[3,54],"on":[4,55,71,79],"random":[5,85,105],"forest":[6,86,106],"proximity":[7,76,96,198],"distance":[8,28,37,77,173,199,203],"(PD)":[9],"is":[10,30,91],"used":[11,210],"to":[12,17,43,93,211],"screen":[13],"the":[14,33,51,60,63,72,75,80,84,95,100,104,110,113,125,135,139,143,158,170,172,175,179,182,184,188,193,202,213],"test":[15,49,131,176],"set":[16],"improve":[18],"protein\u2013protein":[19],"interaction":[20],"site":[21],"(PPIS)":[22],"prediction.":[23],"The":[24],"assessment":[25],"of":[26,39,83,103,112,145,187,215],"a":[27,36],"metric":[29],"done":[31],"under":[32],"assumption":[34],"that":[35,59,74,169,192],"definition":[38,200],"higher":[40,44],"quality":[41],"leads":[42],"classification.":[45],"On":[46,128],"an":[47,88],"independent":[48,130],"set,":[50,142],"numerical":[52,166],"analysis":[53],"statistical":[56],"inference":[57],"shows":[58],"PD":[61,117,136,207],"has":[62],"advantage":[64],"over":[65],"Mahalanobis":[66],"and":[67,120,151,157,178,201],"Cosine":[68],"distance.":[69],"Based":[70],"fact":[73],"depends":[78],"tree":[81,101],"composition":[82,102],"model,":[87],"iterative":[89,126,194],"designed":[92],"optimize":[94,197],"distance,":[97],"which":[98],"adjusts":[99],"model":[107],"by":[108,124,138,206],"adjusting":[109],"size":[111],"training":[114,141,180],"set.":[115],"Two":[116],"metrics,":[118],"75PD":[119,146],"50PD,":[121],"are":[122],"obtained":[123],"method.":[127],"two":[129],"sets,":[132],"compared":[133],"with":[134],"produced":[137],"original":[140],"values":[144],"in":[147],"Matthews":[148],"correlation":[149],"coefficient":[150],"F":[152],"1":[153],"score":[154],"were":[155,162],"higher,":[156],"differences":[159],"between":[160,174],"them":[161],"statistically":[163],"significant.":[164],"All":[165],"experiments":[167],"show":[168],"closer":[171],"data":[177],"data,":[181],"better":[183],"prediction":[185,216],"results":[186],"predictor.":[189],"These":[190],"indicate":[191,212],"can":[196,208],"information":[204],"provided":[205],"be":[209],"reliability":[214],"results.":[217]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}