{"id":"https://openalex.org/W2066123704","doi":"https://doi.org/10.1142/s0219720006002119","title":"IMPROVING THE SENSITIVITY AND SPECIFICITY OF PROTEIN HOMOLOGY SEARCH BY INCORPORATING PREDICTED SECONDARY STRUCTURES","display_name":"IMPROVING THE SENSITIVITY AND SPECIFICITY OF PROTEIN HOMOLOGY SEARCH BY INCORPORATING PREDICTED SECONDARY STRUCTURES","publication_year":2006,"publication_date":"2006-06-01","ids":{"openalex":"https://openalex.org/W2066123704","doi":"https://doi.org/10.1142/s0219720006002119","mag":"2066123704","pmid":"https://pubmed.ncbi.nlm.nih.gov/16960971"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720006002119","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720006002119","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/A5100749734","display_name":"Bin Ma","orcid":"https://orcid.org/0000-0002-9030-7393"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"BIN MA","raw_affiliation_strings":["Computer Science Department, University of Western Ontario, London, ON N6A 5B7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Western Ontario, London, ON N6A 5B7, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017368130","display_name":"Lieyu Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"LIEYU WU","raw_affiliation_strings":["Computer Science Department, University of Western Ontario, London, ON N6A 5B7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Western Ontario, London, ON N6A 5B7, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081729547","display_name":"Kaizhong Zhang","orcid":"https://orcid.org/0000-0003-1734-5921"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"KAIZHONG ZHANG","raw_affiliation_strings":["Computer Science Department, University of Western Ontario, London, ON N6A 5B7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Western Ontario, London, ON N6A 5B7, Canada","institution_ids":["https://openalex.org/I125749732"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I125749732"],"apc_list":null,"apc_paid":null,"fwci":0.2701,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.57511363,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"04","issue":"03","first_page":"709","last_page":"720"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9986000061035156,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9986000061035156,"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":0.9976999759674072,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9968000054359436,"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/homology","display_name":"Homology (biology)","score":0.7289795279502869},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.6438361406326294},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4971330463886261},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.47411516308784485},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45416292548179626},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43997716903686523},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.4124906659126282},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3642721176147461},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3587355613708496},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3365561068058014},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2861349582672119},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2224595546722412},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.1546517312526703},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1327606439590454},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08234283328056335}],"concepts":[{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.7289795279502869},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.6438361406326294},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4971330463886261},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.47411516308784485},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45416292548179626},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43997716903686523},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.4124906659126282},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3642721176147461},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3587355613708496},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3365561068058014},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2861349582672119},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2224595546722412},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.1546517312526703},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1327606439590454},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08234283328056335},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0}],"mesh":[{"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":2,"locations":[{"id":"doi:10.1142/s0219720006002119","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720006002119","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:16960971","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16960971","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W631149005","https://openalex.org/W1502621331","https://openalex.org/W1533038909","https://openalex.org/W1588600188","https://openalex.org/W1955121107","https://openalex.org/W1975989487","https://openalex.org/W1985818354","https://openalex.org/W1989977771","https://openalex.org/W2029195137","https://openalex.org/W2055043387","https://openalex.org/W2087064593","https://openalex.org/W2102677343","https://openalex.org/W2104972430","https://openalex.org/W2105840826","https://openalex.org/W2118848941","https://openalex.org/W2119587711","https://openalex.org/W2128591967","https://openalex.org/W2131724426","https://openalex.org/W2131989567","https://openalex.org/W2142375194","https://openalex.org/W2143210482","https://openalex.org/W2152520756","https://openalex.org/W2153187042","https://openalex.org/W2158714788","https://openalex.org/W2160672912"],"related_works":["https://openalex.org/W2928838901","https://openalex.org/W4206825711","https://openalex.org/W2253761889","https://openalex.org/W3204091482","https://openalex.org/W2081601977","https://openalex.org/W2114568928","https://openalex.org/W1543174845","https://openalex.org/W3086268169","https://openalex.org/W2119378770","https://openalex.org/W2033650210"],"abstract_inverted_index":{"In":[0],"this":[1,50],"paper,":[2],"we":[3],"improve":[4,34],"the":[5,10,13,25,35,42,45,56,61],"homology":[6,36],"search":[7,37],"performance":[8],"by":[9,52,60],"combination":[11,27],"of":[12,28,41],"predicted":[14,29],"protein":[15,19],"secondary":[16,30],"structures":[17,31],"and":[18],"sequences.":[20],"Previous":[21],"research":[22],"suggested":[23],"that":[24],"straightforward":[26],"did":[32],"not":[33],"performance,":[38],"mostly":[39],"because":[40],"errors":[43],"in":[44],"structure":[46],"prediction.":[47],"We":[48],"solved":[49],"problem":[51],"taking":[53],"into":[54],"account":[55],"confidence":[57],"scores":[58],"output":[59],"prediction":[62],"programs.":[63]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
