{"id":"https://openalex.org/W2117499714","doi":"https://doi.org/10.1109/csb.2003.1227314","title":"Towards index-based similarity search for protein structure databases","display_name":"Towards index-based similarity search for protein structure databases","publication_year":2004,"publication_date":"2004-03-23","ids":{"openalex":"https://openalex.org/W2117499714","doi":"https://doi.org/10.1109/csb.2003.1227314","mag":"2117499714","pmid":"https://pubmed.ncbi.nlm.nih.gov/16452789"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2003.1227314","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227314","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-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/A5056984579","display_name":"Orhan \u00c7amo\u01e7lu","orcid":null},"institutions":[{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"O. Camoglu","raw_affiliation_strings":["Department of Computer Science, University of California, Santa Barbara, CA, USA","Dept. of Comput. Sci., California Univ., Santa Barbara, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Santa Barbara, CA, USA","institution_ids":["https://openalex.org/I154570441"]},{"raw_affiliation_string":"Dept. of Comput. Sci., California Univ., Santa Barbara, CA, USA","institution_ids":["https://openalex.org/I154570441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091769289","display_name":"Tamer Kahveci","orcid":"https://orcid.org/0000-0002-4403-8612"},"institutions":[{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. Kahveci","raw_affiliation_strings":["Department of Computer Science, University of California, Santa Barbara, CA, USA","Dept. of Comput. Sci., California Univ., Santa Barbara, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Santa Barbara, CA, USA","institution_ids":["https://openalex.org/I154570441"]},{"raw_affiliation_string":"Dept. of Comput. Sci., California Univ., Santa Barbara, CA, USA","institution_ids":["https://openalex.org/I154570441"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036639779","display_name":"Ambuj K. Singh","orcid":"https://orcid.org/0000-0002-1997-7140"},"institutions":[{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A.K. Singh","raw_affiliation_strings":["Department of Computer Science, University of California, Santa Barbara, CA, USA","Dept. of Comput. Sci., California Univ., Santa Barbara, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Santa Barbara, CA, USA","institution_ids":["https://openalex.org/I154570441"]},{"raw_affiliation_string":"Dept. of Comput. Sci., California Univ., Santa Barbara, CA, USA","institution_ids":["https://openalex.org/I154570441"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5056984579"],"corresponding_institution_ids":["https://openalex.org/I154570441"],"apc_list":null,"apc_paid":null,"fwci":5.1425,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.95884688,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"2","issue":null,"first_page":"148","last_page":"158"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11106","display_name":"Data Management and Algorithms","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"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/T11106","display_name":"Data Management and Algorithms","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"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/T11269","display_name":"Algorithms and Data Compression","score":0.9882000088691711,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9837999939918518,"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/computer-science","display_name":"Computer science","score":0.7040532231330872},{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.6494296789169312},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.645132303237915},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6355125308036804},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.6334638595581055},{"id":"https://openalex.org/keywords/nearest-neighbor-search","display_name":"Nearest neighbor search","score":0.6126666069030762},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5880761742591858},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5319958329200745},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.45681867003440857},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.4418230652809143},{"id":"https://openalex.org/keywords/feature-vector","display_name":"Feature vector","score":0.425912082195282},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3923093378543854},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3447068929672241},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3283516764640808},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.06980913877487183}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7040532231330872},{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.6494296789169312},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.645132303237915},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6355125308036804},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.6334638595581055},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.6126666069030762},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5880761742591858},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5319958329200745},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.45681867003440857},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.4418230652809143},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.425912082195282},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3923093378543854},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3447068929672241},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3283516764640808},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.06980913877487183},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","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":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1109/csb.2003.1227314","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227314","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"},{"id":"pmid:16452789","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16452789","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":"Proceedings. IEEE Computer Society Bioinformatics Conference","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.4.8924","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.4.8924","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.ucsb.edu/~tamer/papers/csb2003.ps","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W42190837","https://openalex.org/W1520321564","https://openalex.org/W1965907701","https://openalex.org/W1972148314","https://openalex.org/W1975453400","https://openalex.org/W1979147581","https://openalex.org/W1988874269","https://openalex.org/W1993273781","https://openalex.org/W2022058405","https://openalex.org/W2024519892","https://openalex.org/W2050330741","https://openalex.org/W2097471670","https://openalex.org/W2124363644","https://openalex.org/W2127054268","https://openalex.org/W2144071905","https://openalex.org/W2151135734","https://openalex.org/W2152024417","https://openalex.org/W2152326664","https://openalex.org/W2427045451","https://openalex.org/W2753710282","https://openalex.org/W4213366719","https://openalex.org/W4239426826","https://openalex.org/W6601694875","https://openalex.org/W6631239882"],"related_works":["https://openalex.org/W3024364549","https://openalex.org/W1949910768","https://openalex.org/W1480566255","https://openalex.org/W190832529","https://openalex.org/W2254397067","https://openalex.org/W2013685631","https://openalex.org/W1610355325","https://openalex.org/W1882921205","https://openalex.org/W2129925734","https://openalex.org/W1498488440"],"abstract_inverted_index":{"We":[0,83],"propose":[1],"two":[2,108],"methods":[3],"for":[4],"finding":[5,43],"similarities":[6],"in":[7,51],"protein":[8,50,53,73,109],"structure":[9],"databases.":[10],"Our":[11,36,100],"techniques":[12,121],"extract":[13],"feature":[14,26],"vectors":[15,27],"on":[16],"triplets":[17],"of":[18,23,42,94,106,126],"SSEs":[19],"(Secondary":[20],"Structure":[21],"Elements)":[22],"proteins.":[24],"These":[25,65],"are":[28,67],"then":[29,68],"indexed":[30],"using":[31,61,74,97],"a":[32,47,52,75,86,95],"multidimensional":[33],"index":[34,63],"structure.":[35,64],"first":[37],"technique":[38,56,102],"considers":[39,103],"the":[40,62,71,92,98,104,123,134],"problem":[41,105],"proteins":[44,60,66],"similar":[45],"to":[46,70,90,111,129],"given":[48],"query":[49,72],"dataset.":[54],"This":[55],"quickly":[57],"finds":[58],"promising":[59],"aligned":[69],"popular":[76],"pairwise":[77],"alignment":[78],"tool":[79],"such":[80],"as":[81],"VAST.":[82],"also":[84],"develop":[85],"novel":[87],"statistical":[88],"model":[89],"estimate":[91],"goodness":[93],"match":[96],"SSEs.":[99],"second":[101],"joining":[107],"datasets":[110],"find":[112],"an":[113],"all-to-all":[114],"similarity.":[115],"Experimental":[116],"results":[117],"show":[118],"that":[119],"our":[120],"improve":[122],"pruning":[124],"time":[125],"VAST":[127],"3":[128],"3.5":[130],"times":[131],"while":[132],"keeping":[133],"sensitivity":[135],"similar.":[136]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
