{"id":"https://openalex.org/W2159849240","doi":"https://doi.org/10.1093/bioinformatics/btr249","title":"Multi-view methods for protein structure comparison using latent dirichlet allocation","display_name":"Multi-view methods for protein structure comparison using latent dirichlet allocation","publication_year":2011,"publication_date":"2011-06-14","ids":{"openalex":"https://openalex.org/W2159849240","doi":"https://doi.org/10.1093/bioinformatics/btr249","mag":"2159849240","pmid":"https://pubmed.ncbi.nlm.nih.gov/21685102"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr249","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr249","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/13/i61/447067/btr249.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/13/i61/447067/btr249.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063682484","display_name":"S. Shivashankar","orcid":null},"institutions":[{"id":"https://openalex.org/I24676775","display_name":"Indian Institute of Technology Madras","ror":"https://ror.org/03v0r5n49","country_code":"IN","type":"education","lineage":["https://openalex.org/I24676775"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"S. Shivashankar","raw_affiliation_strings":["Department of Computer Science and Engineering, IIT Madras, Chennai-600 036"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, IIT Madras, Chennai-600 036","institution_ids":["https://openalex.org/I24676775"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034553104","display_name":"Sandeep Srivathsan","orcid":"https://orcid.org/0000-0002-1586-1677"},"institutions":[{"id":"https://openalex.org/I24676775","display_name":"Indian Institute of Technology Madras","ror":"https://ror.org/03v0r5n49","country_code":"IN","type":"education","lineage":["https://openalex.org/I24676775"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"S. Srivathsan","raw_affiliation_strings":["Department of Computer Science and Engineering, IIT Madras, Chennai-600 036"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, IIT Madras, Chennai-600 036","institution_ids":["https://openalex.org/I24676775"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009374923","display_name":"Balaraman Ravindran","orcid":"https://orcid.org/0000-0002-5364-7639"},"institutions":[{"id":"https://openalex.org/I24676775","display_name":"Indian Institute of Technology Madras","ror":"https://ror.org/03v0r5n49","country_code":"IN","type":"education","lineage":["https://openalex.org/I24676775"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"B. Ravindran","raw_affiliation_strings":["Department of Computer Science and Engineering, IIT Madras, Chennai-600 036"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, IIT Madras, Chennai-600 036","institution_ids":["https://openalex.org/I24676775"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048099130","display_name":"Ashish V. Tendulkar","orcid":null},"institutions":[{"id":"https://openalex.org/I24676775","display_name":"Indian Institute of Technology Madras","ror":"https://ror.org/03v0r5n49","country_code":"IN","type":"education","lineage":["https://openalex.org/I24676775"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Ashish V. Tendulkar","raw_affiliation_strings":["Department of Computer Science and Engineering, IIT Madras, Chennai-600 036"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, IIT Madras, Chennai-600 036","institution_ids":["https://openalex.org/I24676775"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5048099130"],"corresponding_institution_ids":["https://openalex.org/I24676775"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":0.3739,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.61452445,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"27","issue":"13","first_page":"i61","last_page":"i68"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.5914000272750854,"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":0.5914000272750854,"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":0.26570001244544983,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.038600001484155655,"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/latent-dirichlet-allocation","display_name":"Latent Dirichlet allocation","score":0.7701176404953003},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7657169103622437},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7541991472244263},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.7530224323272705},{"id":"https://openalex.org/keywords/topic-model","display_name":"Topic model","score":0.466943621635437},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42864513397216797},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3594772219657898},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32714369893074036}],"concepts":[{"id":"https://openalex.org/C500882744","wikidata":"https://www.wikidata.org/wiki/Q269236","display_name":"Latent Dirichlet allocation","level":3,"score":0.7701176404953003},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7657169103622437},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7541991472244263},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.7530224323272705},{"id":"https://openalex.org/C171686336","wikidata":"https://www.wikidata.org/wiki/Q3532085","display_name":"Topic model","level":2,"score":0.466943621635437},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42864513397216797},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3594772219657898},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32714369893074036},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btr249","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr249","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/13/i61/447067/btr249.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21685102","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21685102","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3117356","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3117356","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.308.4433","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.308.4433","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cse.iitm.ac.in/~ravi//papers/Shivashankar_ISMB_11.pdf","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:27/13/i61","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/13/i61","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr249","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr249","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/13/i61/447067/btr249.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2159849240.pdf","grobid_xml":"https://content.openalex.org/works/W2159849240.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1513073936","https://openalex.org/W1532325895","https://openalex.org/W1575541347","https://openalex.org/W1880262756","https://openalex.org/W1969850472","https://openalex.org/W1979147581","https://openalex.org/W2001082470","https://openalex.org/W2020999234","https://openalex.org/W2023790301","https://openalex.org/W2050537942","https://openalex.org/W2058731099","https://openalex.org/W2071037669","https://openalex.org/W2087596922","https://openalex.org/W2099475859","https://openalex.org/W2100126267","https://openalex.org/W2114317416","https://openalex.org/W2131204071","https://openalex.org/W2137146016","https://openalex.org/W2151785844","https://openalex.org/W2152326664","https://openalex.org/W2157965775","https://openalex.org/W2158630348","https://openalex.org/W2410255781","https://openalex.org/W4213009331","https://openalex.org/W4238071843","https://openalex.org/W6639619044","https://openalex.org/W6714452398"],"related_works":["https://openalex.org/W2769501189","https://openalex.org/W4315588616","https://openalex.org/W4312773271","https://openalex.org/W2888805565","https://openalex.org/W2962686197","https://openalex.org/W3005513013","https://openalex.org/W2207653751","https://openalex.org/W2611137333","https://openalex.org/W4389543811","https://openalex.org/W4291700620"],"abstract_inverted_index":{"MOTIVATION:":[0],"With":[1],"rapidly":[2],"expanding":[3],"protein":[4,14,26,83],"structure":[5,27],"databases,":[6],"efficiently":[7],"retrieving":[8],"structures":[9,41,84],"similar":[10],"to":[11,46,67,95,108],"a":[12],"given":[13],"is":[15,94],"an":[16,79],"important":[17,92],"problem.":[18],"It":[19],"involves":[20],"two":[21],"major":[22],"issues:":[23],"(i)":[24],"effective":[25,44],"representation":[28,63,81,128],"that":[29,117,144],"captures":[30],"inherent":[31],"relationship":[32],"between":[33,39],"fragments":[34,62],"and":[35,42,121,129,139],"facilitates":[36],"efficient":[37],"comparison":[38],"the":[40,68,126,133,145],"(ii)":[43],"framework":[45,116,131],"address":[47],"different":[48],"retrieval":[49,71,122,130],"requirements.":[50],"Recently,":[51],"researchers":[52],"proposed":[53,127,146],"vector":[54],"space":[55],"model":[56],"of":[57,61,82],"proteins":[58],"using":[59,85],"bag":[60],"(FragBag),":[64],"which":[65],"corresponds":[66],"basic":[69],"information":[70],"model.":[72,90],"RESULTS:":[73],"In":[74,106],"this":[75],"article,":[76],"we":[77,112],"propose":[78,113],"improved":[80],"latent":[86],"dirichlet":[87],"allocation":[88],"topic":[89],"Another":[91],"requirement":[93],"retrieve":[96],"proteins,":[97],"whether":[98],"they":[99],"are":[100],"either":[101],"close":[102],"or":[103],"remote":[104],"homologs.":[105],"order":[107],"meet":[109],"diverse":[110],"objectives,":[111],"multi-viewpoint":[114],"based":[115],"combines":[118],"multiple":[119],"representations":[120],"techniques.":[123],"We":[124],"compare":[125],"on":[132],"benchmark":[134],"dataset":[135],"developed":[136],"by":[137],"Kolodny":[138],"co-workers.":[140],"The":[141],"results":[142],"indicate":[143],"techniques":[147],"outperform":[148],"state-of-the-art":[149],"methods.":[150],"AVAILABILITY:":[151],"http://www.cse.iitm.ac.in/~ashishvt/research/protein-lda/.":[152],"CONTACT:":[153],"ashishvt@cse.iitm.ac.in.":[154]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
