{"id":"https://openalex.org/W2109199414","doi":"https://doi.org/10.1093/bioinformatics/bti135","title":"Predicting fold novelty based on ProtoNet hierarchical classification","display_name":"Predicting fold novelty based on ProtoNet hierarchical classification","publication_year":2004,"publication_date":"2004-11-11","ids":{"openalex":"https://openalex.org/W2109199414","doi":"https://doi.org/10.1093/bioinformatics/bti135","mag":"2109199414","pmid":"https://pubmed.ncbi.nlm.nih.gov/15539447"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti135","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti135","pdf_url":null,"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":null,"license_id":null,"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":"green","oa_url":"https://ink.library.smu.edu.sg/sis_research/86","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005319261","display_name":"Ilona Kifer","orcid":null},"institutions":[{"id":"https://openalex.org/I2800263366","display_name":"Jerusalem Institute for Israel Studies","ror":"https://ror.org/02zax3c17","country_code":"IL","type":"nonprofit","lineage":["https://openalex.org/I2800263366"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Ilona Kifer","raw_affiliation_strings":["Department of Biological Chemistry, Institute of Life Sciences Jerusalem 91904, Israel","Dept. of Biological Chemistry, Institute of Life Sciences, Jerusalem, 91904, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry, Institute of Life Sciences Jerusalem 91904, Israel","institution_ids":["https://openalex.org/I2800263366"]},{"raw_affiliation_string":"Dept. of Biological Chemistry, Institute of Life Sciences, Jerusalem, 91904, Israel","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043491853","display_name":"Ori Sasson","orcid":null},"institutions":[{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Ori Sasson","raw_affiliation_strings":["School of Computer Science and Engineering, The Hebrew University Jerusalem, 91904, Israel"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, The Hebrew University Jerusalem, 91904, Israel","institution_ids":["https://openalex.org/I197251160"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085924022","display_name":"Michal Linial","orcid":"https://orcid.org/0000-0002-9357-4526"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Michal Linial","raw_affiliation_strings":["Dept. of Biological Chemistry, Institute of Life Sciences, Jerusalem, 91904, Israel"],"affiliations":[{"raw_affiliation_string":"Dept. of Biological Chemistry, Institute of Life Sciences, Jerusalem, 91904, Israel","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5005319261"],"corresponding_institution_ids":["https://openalex.org/I2800263366"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.479,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.62385944,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"21","issue":"7","first_page":"1020","last_page":"1027"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9975000023841858,"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":0.9975000023841858,"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/T11512","display_name":"Anomaly Detection Techniques and Applications","score":0.9789999723434448,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9702000021934509,"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/novelty","display_name":"Novelty","score":0.7900007963180542},{"id":"https://openalex.org/keywords/fold","display_name":"Fold (higher-order function)","score":0.771239161491394},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5731285810470581},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43440645933151245},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32906824350357056},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.09641033411026001}],"concepts":[{"id":"https://openalex.org/C2778738651","wikidata":"https://www.wikidata.org/wiki/Q16546687","display_name":"Novelty","level":2,"score":0.7900007963180542},{"id":"https://openalex.org/C53942344","wikidata":"https://www.wikidata.org/wiki/Q951651","display_name":"Fold (higher-order function)","level":2,"score":0.771239161491394},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5731285810470581},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43440645933151245},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32906824350357056},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.09641033411026001},{"id":"https://openalex.org/C77805123","wikidata":"https://www.wikidata.org/wiki/Q161272","display_name":"Social psychology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","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":"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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"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":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"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":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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti135","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti135","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15539447","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15539447","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":null},{"id":"pmh:oai:ink.library.smu.edu.sg:sis_research-1085","is_oa":true,"landing_page_url":"https://ink.library.smu.edu.sg/sis_research/86","pdf_url":null,"source":{"id":"https://openalex.org/S4377196871","display_name":"Institutional Knowledge (InK) - Institutional Knowledge at Singapore Management University (Singapore Management University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79891267","host_organization_name":"Singapore Management University","host_organization_lineage":["https://openalex.org/I79891267"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://dx.doi.org/10.1093/bioinformatics/bti135","raw_type":"Journal Article"}],"best_oa_location":{"id":"pmh:oai:ink.library.smu.edu.sg:sis_research-1085","is_oa":true,"landing_page_url":"https://ink.library.smu.edu.sg/sis_research/86","pdf_url":null,"source":{"id":"https://openalex.org/S4377196871","display_name":"Institutional Knowledge (InK) - Institutional Knowledge at Singapore Management University (Singapore Management University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79891267","host_organization_name":"Singapore Management University","host_organization_lineage":["https://openalex.org/I79891267"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://dx.doi.org/10.1093/bioinformatics/bti135","raw_type":"Journal Article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.46000000834465027}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321950","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1513621883","https://openalex.org/W1534270226","https://openalex.org/W1576520375","https://openalex.org/W1582255757","https://openalex.org/W1604726175","https://openalex.org/W1986155816","https://openalex.org/W1992305340","https://openalex.org/W1997268601","https://openalex.org/W1999121134","https://openalex.org/W2008390237","https://openalex.org/W2020481171","https://openalex.org/W2083339788","https://openalex.org/W2084523421","https://openalex.org/W2095318832","https://openalex.org/W2096540816","https://openalex.org/W2107302432","https://openalex.org/W2108758729","https://openalex.org/W2109781945","https://openalex.org/W2115138247","https://openalex.org/W2115848690","https://openalex.org/W2117077088","https://openalex.org/W2118651376","https://openalex.org/W2130479394","https://openalex.org/W2135144811","https://openalex.org/W2136766277","https://openalex.org/W2140244239","https://openalex.org/W2141737941","https://openalex.org/W2146189537","https://openalex.org/W2147556320","https://openalex.org/W2153187042","https://openalex.org/W2157975034","https://openalex.org/W2158714788","https://openalex.org/W2165206687","https://openalex.org/W2166278492","https://openalex.org/W6926424358"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2381242807","https://openalex.org/W2751208925","https://openalex.org/W3126131230","https://openalex.org/W2347541121","https://openalex.org/W4288804799","https://openalex.org/W2080951048","https://openalex.org/W3089617106","https://openalex.org/W2033914206","https://openalex.org/W2042327336"],"abstract_inverted_index":{"We":[0,84],"develop":[1],"a":[2,8,14,24],"method":[3,21,89,105,111],"that":[4,42,44,72,86],"assigns":[5],"each":[6],"protein":[7,35],"likelihood":[9],"of":[10,26,33,77,93],"it":[11],"belonging":[12],"to":[13,57,59,82,102],"new,":[15],"yet":[16],"undetermined,":[17],"structural":[18],"superfamily.":[19],"The":[20,62],"relies":[22],"on":[23],"variant":[25],"ProtoNet,":[27],"an":[28],"automatic":[29],"hierarchical":[30],"classification":[31],"scheme":[32],"all":[34],"sequences":[36],"from":[37,47,69],"SwissProt.":[38],"Our":[39],"results":[40,63],"show":[41,85],"proteins":[43],"are":[45,54,64,95],"remote":[46],"solved":[48,79],"structures":[49,80],"in":[50,97,115],"the":[51,78,91],"ProtoNet":[52,94],"hierarchy":[53],"more":[55],"likely":[56],"belong":[58],"new":[60,88,99,118],"superfamilies.":[61,119],"validated":[65],"against":[66],"SCOP":[67],"releases":[68],"recent":[70],"years":[71],"account":[73],"for":[74],"about":[75],"half":[76],"known":[81],"date.":[83],"our":[87,103,110],"and":[90],"representation":[92],"superior":[96],"detecting":[98,116],"targets,":[100],"compared":[101],"previous":[104],"using":[106],"ProtoMap":[107],"classification.":[108],"Furthermore,":[109],"outperforms":[112],"PSI-BLAST":[113],"search":[114],"potential":[117]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
